I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 5 07:36:00 -12 2022 I: pbuilder-time-stamp: 1659728160 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iqtree_1.6.9+dfsg-1.dsc] I: copying [./iqtree_1.6.9+dfsg.orig.tar.xz] I: copying [./iqtree_1.6.9+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 2 01:51:35 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iqtree_1.6.9+dfsg-1.dsc dpkg-source: info: extracting iqtree in iqtree-1.6.9+dfsg dpkg-source: info: unpacking iqtree_1.6.9+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_1.6.9+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/39253/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6534fbfd2ca94614bace22c8e1a0af23' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='39253' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/pbuilderrc_udrE --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/b1 --logfile b1/build.log iqtree_1.6.9+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 24 02:46 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/39253/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), cmake, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libsprng2-dev; however: Package libsprng2-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbsd0{a} libcroco3{a} libcurl4{a} libedit2{a} libeigen3-dev{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgmp-dev{a} libgmpxx4ldbl{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libprocps7{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsprng2{a} libsprng2-dev{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} lsb-base{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} procps{a} sensible-utils{a} time{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 39.4 MB of archives. After unpacking 152 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 ibverbs-providers amd64 22.1-1 [187 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libeigen3-dev all 3.3.7-1 [850 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libgmpxx4ldbl amd64 2:6.1.2+dfsg-4 [22.9 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libgmp-dev amd64 2:6.1.2+dfsg-4 [628 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libltdl-dev amd64 2.4.6-9 [162 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libhwloc-dev amd64 1.11.12-3 [175 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libibverbs-dev amd64 22.1-1 [362 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libsprng2 amd64 2.0a-12 [75.7 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libsprng2-dev amd64 2.0a-12 [79.2 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get: 100 http://deb.debian.org/debian buster/main amd64 time amd64 1.7-25.1+b1 [31.6 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 39.4 MB in 1s (70.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/iqtree-1.6.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 1.6.9+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/nclextra /build/iqtree-1.6.9+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/whtest /build/iqtree-1.6.9+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/sprng /build/iqtree-1.6.9+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/vectorclass /build/iqtree-1.6.9+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target sprng Scanning dependencies of target gsl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target ncl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target vectorclass Scanning dependencies of target whtest make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build Scanning dependencies of target kernelfma make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target kernelsse make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build Scanning dependencies of target kernelavx Scanning dependencies of target nclextra make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build Scanning dependencies of target pll [ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o [ 2%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c [ 4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp [ 4%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o [ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c [ 6%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 7%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o [ 8%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp [ 10%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c [ 12%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp [ 15%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c [ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o [ 15%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp [ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c [ 15%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 17%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' /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 [ 17%] Built target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 18%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp [ 19%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c [ 19%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c [ 19%] Built target sprng [ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 21%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ [ 21%] Linking CXX static library libgsl.a cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 22%] Built target gsl [ 22%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c [ 23%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ [ 24%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp [ 27%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c [ 27%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 28%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c [ 28%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c [ 29%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ [ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o [ 31%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 [ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp [ 32%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 [ 32%] Built target pllavx /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp [ 33%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o /usr/bin/ranlib liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c [ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c [ 34%] Built target lbfgsb [ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp [ 37%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 37%] Built target whtest make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 38%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 39%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp [ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c [ 41%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c [ 42%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp [ 43%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 44%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c [ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 45%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp [ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c [ 47%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 47%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp [ 49%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c [ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp [ 49%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 50%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 53%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake [ 54%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake /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 cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libncl.a /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 54%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= [ 54%] Built target pll Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp [ 59%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 59%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pda /build/iqtree-1.6.9+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 59%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o [ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 68%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 77%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 78%] Built target pda [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 84%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target alignment [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target kernelsse [ 84%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target kernelfma [ 84%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/tree /build/iqtree-1.6.9+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 87%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 97%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build Scanning dependencies of target pllavx Scanning dependencies of target nclextra make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target vectorclass Scanning dependencies of target ncl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp Scanning dependencies of target kernelavx [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp Scanning dependencies of target kernelsse [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c [ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp [ 3%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp [ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o [ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp Scanning dependencies of target pll cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp [ 6%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 7%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp [ 8%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o Scanning dependencies of target kernelfma cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build [ 9%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c [ 11%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp [ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c [ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 15%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 15%] Linking CXX static library libgsl.a [ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o [ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a /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 make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/ranlib libgsl.a [ 17%] Built target vectorclass [ 17%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c [ 18%] Built target gsl [ 18%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o [ 19%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 20%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake [ 21%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a [ 21%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 21%] Built target sprng [ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ [ 23%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 23%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c [ 24%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c [ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp [ 27%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 28%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c [ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 29%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 29%] Built target pllavx [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c [ 31%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c [ 31%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c [ 32%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 32%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 33%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c [ 34%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 35%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 35%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 36%] Building C object pll/CMakeFiles/pll.dir/stack.c.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c [ 37%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 37%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c [ 38%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp [ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 39%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 40%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c [ 41%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp [ 44%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 44%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp [ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp [ 48%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake [ 49%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /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 [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o /usr/bin/ranlib libpll.a cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp [ 50%] Linking CXX static library libnclextra.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake [ 50%] Built target whtest [ 50%] Built target pll cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp /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 [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 51%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 51%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o [ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 64%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 64%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ [ 68%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/model /build/iqtree-1.6.9+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 68%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 68%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 73%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 73%] Built target pda [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 84%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target alignment [ 84%] 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]: 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CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/tree /build/iqtree-1.6.9+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/mympi.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/gsl /build/iqtree-1.6.9+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/ncl /build/iqtree-1.6.9+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target mympi make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend Scanning dependencies of target ncl Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target lbfgsb make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 0%] Building CXX object CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/TreeCollection.cpp make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build Scanning dependencies of target kernelsse make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 1%] Building CXX object CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/ObjectStream.cpp make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp Scanning dependencies of target nclextra [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o [ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o [ 4%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp [ 4%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp [ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp [ 6%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o [ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp [ 8%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o Scanning dependencies of target pll cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c [ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 9%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 10%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c [ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend [ 11%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 12%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c [ 13%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c [ 13%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 14%] Linking CXX static library libgsl.a cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 15%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ [ 15%] Built target gsl make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 15%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c [ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp [ 17%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 17%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 18%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 19%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 19%] Built target vectorclass In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c [ 19%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o [ 20%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c [ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ [ 22%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o [ 23%] Building C object pll/CMakeFiles/pll.dir/models.c.o [ 23%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 23%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 23%] Built target sprng [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp [ 25%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c [ 25%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c [ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ [ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp [ 29%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c [ 29%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o [ 30%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 30%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 31%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp [ 32%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 32%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 33%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 34%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o [ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c [ 35%] Built target pllavx [ 35%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 35%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c [ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o [ 36%] Linking CXX static library libmympi.a /usr/bin/cmake -P CMakeFiles/mympi.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/mympi.dir/link.txt --verbose=1 /usr/bin/ar qc libmympi.a CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o /usr/bin/ranlib libmympi.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 36%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c [ 36%] Built target mympi [ 37%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 37%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 40%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o [ 40%] Building C object pll/CMakeFiles/pll.dir/trash.c.o /usr/bin/ranlib libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 41%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c [ 41%] Built target whtest [ 42%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 43%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o [ 45%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp [ 46%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 48%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp /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 [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 49%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp [ 50%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o /usr/bin/ranlib libpll.a cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 51%] Built target pll [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 56%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c [ 57%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 60%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 60%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/alignment /build/iqtree-1.6.9+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ [ 63%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/model /build/iqtree-1.6.9+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o [ 67%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 71%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 71%] Built target pda [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 81%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 81%] Built target alignment [ 81%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 81%] Built target kernelsse [ 82%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 82%] Built target kernelfma [ 83%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 83%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/tree /build/iqtree-1.6.9+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree-mpi -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a libmympi.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo' >> example.short time sh example.short Executing tests using /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp ... + time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: ionos5-amd64 (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy Seed: 215912 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Aug 5 07:42:21 2022 Kernel: AVX - 1 threads (16 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 16 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 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 JC 11923.628 85 24017.255 24066.316 24353.060 2 JC+I 11669.883 86 23511.767 23562.150 23851.522 3 JC+G4 11363.296 86 22898.591 22948.975 23238.346 4 JC+I+G4 11346.433 87 22866.867 22918.597 23210.573 5 JC+R2 11460.283 87 23094.567 23146.297 23438.273 6 JC+R3 11349.557 89 22877.115 22931.605 23228.722 7 JC+R4 11340.087 91 22862.174 22919.516 23221.682 8 JC+R5 11339.948 93 22865.897 22926.187 23233.307 14 F81+F 11927.333 88 24030.666 24083.765 24378.323 15 F81+F+I 11670.259 89 23518.518 23573.008 23870.125 16 F81+F+G4 11358.529 89 22895.058 22949.547 23246.665 17 F81+F+I+G4 11341.895 90 22863.789 22919.694 23219.347 18 F81+F+R2 11457.886 90 23095.773 23151.677 23451.331 19 F81+F+R3 11345.804 92 22875.608 22934.412 23239.067 20 F81+F+R4 11335.393 94 22858.786 22920.585 23230.146 21 F81+F+R5 11335.282 96 22862.564 22927.455 23241.825 27 K2P 11881.076 86 23934.153 23984.537 24273.908 28 K2P+I 11627.075 87 23428.149 23479.879 23771.855 29 K2P+G4 11316.740 87 22807.480 22859.210 23151.186 30 K2P+I+G4 11300.267 88 22776.533 22829.632 23124.190 31 K2P+R2 11416.205 88 23008.409 23061.508 23356.066 32 K2P+R3 11303.971 90 22787.942 22843.846 23143.500 33 K2P+R4 11293.768 92 22771.536 22830.340 23134.995 34 K2P+R5 11293.664 94 22775.327 22837.127 23146.688 40 HKY+F 11884.045 89 23946.090 24000.580 24297.697 41 HKY+F+I 11625.800 90 23431.599 23487.503 23787.157 42 HKY+F+G4 11309.303 90 22798.605 22854.510 23154.163 43 HKY+F+I+G4 11293.017 91 22768.033 22825.376 23127.542 44 HKY+F+R2 11411.536 91 23005.072 23062.415 23364.581 45 HKY+F+R3 11297.610 93 22781.221 22841.510 23148.630 46 HKY+F+R4 11286.412 95 22762.823 22826.157 23138.134 47 HKY+F+R5 11286.351 97 22766.702 22833.178 23149.915 53 TNe 11880.065 87 23934.130 23985.859 24277.835 54 TNe+I 11620.650 88 23417.300 23470.398 23764.956 55 TNe+G4 11315.459 88 22806.918 22860.016 23154.575 56 TNe+I+G4 11298.288 89 22774.575 22829.065 23126.182 57 TNe+R2 11414.812 89 23007.624 23062.114 23359.232 58 TNe+R3 11300.588 91 22783.175 22840.518 23142.684 59 TNe+R4 11290.964 93 22767.928 22828.218 23135.338 60 TNe+R5 11290.801 95 22771.601 22834.935 23146.912 66 TN+F 11882.917 90 23945.834 24001.739 24301.392 67 TN+F+I 11618.509 91 23419.019 23476.361 23778.527 68 TN+F+G4 11307.383 91 22796.766 22854.108 23156.274 69 TN+F+I+G4 11290.263 92 22764.527 22823.331 23127.986 70 TN+F+R2 11409.606 92 23003.211 23062.015 23366.670 71 TN+F+R3 11293.299 94 22774.598 22836.398 23145.959 72 TN+F+R4 11282.625 96 22757.250 22822.142 23136.512 73 TN+F+R5 11282.545 98 22761.089 22829.174 23148.252 79 K3P 11867.490 87 23908.981 23960.711 24252.687 80 K3P+I 11612.745 88 23401.490 23454.588 23749.146 81 K3P+G4 11305.537 88 22787.073 22840.172 23134.730 82 K3P+I+G4 11288.477 89 22754.954 22809.444 23106.561 83 K3P+R2 11401.945 89 22981.891 23036.381 23333.498 84 K3P+R3 11291.942 91 22765.885 22823.227 23125.393 85 K3P+R4 11282.100 93 22750.200 22810.490 23117.610 86 K3P+R5 11282.046 95 22754.092 22817.426 23129.403 92 K3Pu+F 11870.569 90 23921.138 23977.043 24276.696 93 K3Pu+F+I 11611.617 91 23405.233 23462.576 23764.742 94 K3Pu+F+G4 11298.775 91 22779.549 22836.892 23139.058 95 K3Pu+F+I+G4 11281.879 92 22747.758 22806.562 23111.217 96 K3Pu+F+R2 11397.646 92 22979.292 23038.096 23342.751 97 K3Pu+F+R3 11286.226 94 22760.452 22822.251 23131.812 98 K3Pu+F+R4 11275.375 96 22742.751 22807.643 23122.013 99 K3Pu+F+R5 11275.327 98 22746.654 22814.738 23133.817 105 TPM2+F 11883.629 90 23947.257 24003.162 24302.815 106 TPM2+F+I 11625.200 91 23432.400 23489.742 23791.908 107 TPM2+F+G4 11308.868 91 22799.735 22857.078 23159.244 108 TPM2+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 109 TPM2+F+R2 11411.526 92 23007.053 23065.857 23370.512 110 TPM2+F+R3 11297.355 94 22782.711 22844.510 23154.071 111 TPM2+F+R4 11286.270 96 22764.539 22829.431 23143.801 112 TPM2+F+R5 11286.146 98 22768.292 22836.376 23155.455 118 TPM2u+F 11883.629 90 23947.258 24003.162 24302.815 119 TPM2u+F+I 11625.201 91 23432.402 23489.745 23791.911 120 TPM2u+F+G4 11308.867 91 22799.735 22857.077 23159.243 121 TPM2u+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 122 TPM2u+F+R2 11411.527 92 23007.053 23065.857 23370.512 123 TPM2u+F+R3 11297.355 94 22782.710 22844.509 23154.070 124 TPM2u+F+R4 11286.270 96 22764.540 22829.432 23143.802 125 TPM2u+F+R5 11286.143 98 22768.285 22836.370 23155.448 131 TPM3+F 11851.525 90 23883.050 23938.954 24238.608 132 TPM3+F+I 11613.469 91 23408.938 23466.281 23768.447 133 TPM3+F+G4 11305.327 91 22792.654 22849.996 23152.162 134 TPM3+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 135 TPM3+F+R2 11405.175 92 22994.351 23053.155 23357.810 136 TPM3+F+R3 11293.007 94 22774.014 22835.813 23145.374 137 TPM3+F+R4 11283.178 96 22758.356 22823.248 23137.618 138 TPM3+F+R5 11283.049 98 22762.099 22830.183 23149.262 144 TPM3u+F 11851.525 90 23883.050 23938.954 24238.608 145 TPM3u+F+I 11613.469 91 23408.938 23466.281 23768.447 146 TPM3u+F+G4 11305.327 91 22792.655 22849.997 23152.163 147 TPM3u+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 148 TPM3u+F+R2 11405.172 92 22994.345 23053.149 23357.804 149 TPM3u+F+R3 11293.007 94 22774.014 22835.813 23145.374 150 TPM3u+F+R4 11283.172 96 22758.344 22823.236 23137.606 151 TPM3u+F+R5 11283.047 98 22762.095 22830.179 23149.258 157 TIMe 11866.486 88 23908.972 23962.070 24256.629 158 TIMe+I 11606.350 89 23390.699 23445.189 23742.306 159 TIMe+G4 11304.322 89 22786.643 22841.133 23138.250 160 TIMe+I+G4 11286.570 90 22753.139 22809.044 23108.697 161 TIMe+R2 11400.580 90 22981.161 23037.065 23336.718 162 TIMe+R3 11288.530 92 22761.060 22819.864 23124.519 163 TIMe+R4 11279.399 94 22746.797 22808.596 23118.158 164 TIMe+R5 11279.309 96 22750.619 22815.511 23129.880 170 TIM+F 11869.451 91 23920.901 23978.244 24280.410 171 TIM+F+I 11604.362 92 23392.723 23451.527 23756.182 172 TIM+F+G4 11296.948 92 22777.895 22836.699 23141.354 173 TIM+F+I+G4 11279.221 93 22744.442 22804.732 23111.852 174 TIM+F+R2 11395.723 93 22977.446 23037.735 23344.855 175 TIM+F+R3 11281.905 95 22753.810 22817.144 23129.121 176 TIM+F+R4 11271.730 97 22737.460 22803.935 23120.672 177 TIM+F+R5 11271.695 99 22741.389 22811.107 23132.503 183 TIM2e 11879.551 88 23935.102 23988.200 24282.758 184 TIM2e+I 11619.949 89 23417.898 23472.388 23769.506 185 TIM2e+G4 11315.204 89 22808.409 22862.898 23160.016 186 TIM2e+I+G4 11298.141 90 22776.282 22832.187 23131.840 187 TIM2e+R2 11414.742 90 23009.484 23065.388 23365.041 188 TIM2e+R3 11300.473 92 22784.945 22843.750 23148.405 189 TIM2e+R4 11290.833 94 22769.667 22831.466 23141.027 190 TIM2e+R5 11290.739 96 22773.478 22838.370 23152.740 196 TIM2+F 11882.506 91 23947.012 24004.354 24306.520 197 TIM2+F+I 11617.928 92 23419.855 23478.659 23783.314 198 TIM2+F+G4 11306.963 92 22797.925 22856.729 23161.384 199 TIM2+F+I+G4 11289.986 93 22765.972 22826.262 23133.382 200 TIM2+F+R2 11409.581 93 23005.161 23065.451 23372.571 201 TIM2+F+R3 11293.076 95 22776.151 22839.485 23151.462 202 TIM2+F+R4 11282.473 97 22758.946 22825.422 23142.159 203 TIM2+F+R5 11282.402 99 22762.805 22832.523 23153.918 209 TIM3e 11838.747 88 23853.494 23906.592 24201.150 210 TIM3e+I 11602.540 89 23383.080 23437.570 23734.687 211 TIM3e+G4 11307.306 89 22792.612 22847.102 23144.219 212 TIM3e+I+G4 11291.340 90 22762.680 22818.585 23118.238 213 TIM3e+R2 11403.257 90 22986.513 23042.418 23342.071 214 TIM3e+R3 11291.597 92 22767.193 22825.997 23130.652 215 TIM3e+R4 11283.522 94 22755.045 22816.844 23126.405 216 TIM3e+R5 11283.418 96 22758.835 22823.727 23138.097 222 TIM3+F 11850.147 91 23882.293 23939.636 24241.802 223 TIM3+F+I 11606.170 92 23396.339 23455.144 23759.799 224 TIM3+F+G4 11303.297 92 22790.593 22849.397 23154.052 225 TIM3+F+I+G4 11287.023 93 22760.046 22820.336 23127.456 226 TIM3+F+R2 11403.216 93 22992.433 23052.722 23359.842 227 TIM3+F+R3 11288.650 95 22767.299 22830.632 23142.610 228 TIM3+F+R4 11279.141 97 22752.282 22818.757 23135.494 229 TIM3+F+R5 11279.094 99 22756.187 22825.905 23147.301 235 TVMe 11826.121 89 23830.242 23884.732 24181.849 236 TVMe+I 11594.361 90 23368.722 23424.627 23724.280 237 TVMe+G4 11295.606 90 22771.211 22827.116 23126.769 238 TVMe+I+G4 11280.065 91 22742.130 22799.473 23101.639 239 TVMe+R2 11390.331 91 22962.661 23020.004 23322.170 240 TVMe+R3 11281.356 93 22748.713 22809.003 23116.123 241 TVMe+R4 11273.798 95 22737.595 22800.929 23112.906 242 TVMe+R5 11273.698 97 22741.396 22807.871 23124.608 248 TVM+F 11837.769 92 23859.537 23918.341 24222.996 249 TVM+F+I 11599.049 93 23384.097 23444.387 23751.507 250 TVM+F+G4 11292.632 93 22771.264 22831.554 23138.674 251 TVM+F+I+G4 11276.861 94 22741.721 22803.521 23113.082 252 TVM+F+R2 11390.890 94 22969.780 23031.579 23341.140 253 TVM+F+R3 11279.704 96 22751.409 22816.301 23130.671 254 TVM+F+R4 11270.720 98 22737.439 22805.524 23124.602 255 TVM+F+R5 11270.590 100 22741.181 22812.559 23136.245 261 SYM 11824.854 90 23829.707 23885.612 24185.265 262 SYM+I 11587.951 91 23357.902 23415.245 23717.411 263 SYM+G4 11294.178 91 22770.357 22827.699 23129.865 264 SYM+I+G4 11278.013 92 22740.027 22798.831 23103.486 265 SYM+R2 11388.873 92 22961.746 23020.550 23325.205 266 SYM+R3 11277.825 94 22743.649 22805.449 23115.010 267 SYM+R4 11270.756 96 22733.511 22798.403 23112.773 268 SYM+R5 11270.608 98 22737.216 22805.300 23124.379 274 GTR+F 11836.396 93 23858.792 23919.082 24226.202 275 GTR+F+I 11591.768 94 23371.536 23433.336 23742.897 276 GTR+F+G4 11290.699 94 22769.397 22831.197 23140.758 277 GTR+F+I+G4 11274.183 95 22738.365 22801.698 23113.676 278 GTR+F+R2 11389.047 95 22968.093 23031.427 23343.404 279 GTR+F+R3 11275.377 97 22744.753 22811.229 23127.966 280 GTR+F+R4 11266.912 99 22731.824 22801.543 23122.938 281 GTR+F+R5 11266.818 101 22735.637 22808.701 23134.652 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+R4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 33.140 seconds (0h:0m:33s) Wall-clock time for ModelFinder: 34.616 seconds (0h:0m:34s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.955 / LogL: -11295.603 Init pinv, alpha: 0.012, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.077 Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.570 / LogL: -11280.070 Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.568 / LogL: -11280.070 Init pinv, alpha: 0.046, 1.000 / Estimate: 0.085, 1.571 / LogL: -11280.067 Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.569 / LogL: -11280.068 Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.065 Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.575 / LogL: -11280.064 Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.064 Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.065 Optimal pinv,alpha: 0.085, 1.575 / LogL: -11280.064 Parameters optimization took 3.767 sec Computing ML distances based on estimated model parameters... 0.021 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -11256.375 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.895 second Computing log-likelihood of 98 initial trees ... 4.293 seconds Current best score: -11233.108 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.475 Iteration 10 / LogL: -11232.108 / Time: 0h:0m:12s Iteration 20 / LogL: -11225.691 / Time: 0h:0m:16s Finish initializing candidate tree set (14) Current best tree score: -11225.475 / CPU time: 12.229 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 22: -11224.924 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 29: -11224.866 Iteration 30 / LogL: -11224.955 / Time: 0h:0m:21s (0h:1m:13s left) Iteration 40 / LogL: -11224.966 / Time: 0h:0m:27s (0h:1m:1s left) Iteration 50 / LogL: -11228.751 / Time: 0h:0m:33s (0h:0m:53s left) Iteration 60 / LogL: -11228.617 / Time: 0h:0m:38s (0h:0m:44s left) Iteration 70 / LogL: -11225.586 / Time: 0h:0m:42s (0h:0m:36s left) Iteration 80 / LogL: -11228.548 / Time: 0h:0m:47s (0h:0m:29s left) Iteration 90 / LogL: -11225.538 / Time: 0h:0m:51s (0h:0m:22s left) Iteration 100 / LogL: -11225.072 / Time: 0h:0m:55s (0h:0m:16s left) Iteration 110 / LogL: -11225.606 / Time: 0h:0m:59s (0h:0m:10s left) Iteration 120 / LogL: -11228.525 / Time: 0h:1m:3s (0h:0m:4s left) Iteration 130 / LogL: -11225.578 / Time: 0h:1m:7s (0h:0m:-1s left) TREE SEARCH COMPLETED AFTER 130 ITERATIONS / Time: 0h:1m:7s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11224.866 Optimal log-likelihood: -11224.865 Rate parameters: A-C: 1.59715 A-G: 2.70642 A-T: 1.82141 C-G: 2.14210 C-T: 2.70642 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.560 Parameters optimization took 1 rounds (0.062 sec) BEST SCORE FOUND : -11224.865 Total tree length: 12.527 Total number of iterations: 130 CPU time used for tree search: 61.978 sec (0h:1m:1s) Wall-clock time used for tree search: 63.929 sec (0h:1m:3s) Total CPU time used: 65.909 sec (0h:1m:5s) Total wall-clock time used: 67.915 sec (0h:1m:7s) 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: Fri Aug 5 07:44:03 2022 99.07user 0.63system 1:42.56elapsed 97%CPU (0avgtext+0avgdata 14660maxresident)k 0inputs+0outputs (0major+2957minor)pagefaults 0swaps + time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: ionos5-amd64 (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo Seed: 784485 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Aug 5 07:44:03 2022 Kernel: AVX - 2 threads (16 CPU cores detected) Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: Restoring information from model checkpoint file example.phy.model.gz CHECKPOINT: Initial tree restored NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 JC 11923.628 85 24017.255 24066.316 24353.060 2 JC+I 11669.883 86 23511.767 23562.150 23851.522 3 JC+G4 11363.296 86 22898.591 22948.975 23238.346 4 JC+I+G4 11346.433 87 22866.867 22918.597 23210.573 5 JC+R2 11460.283 87 23094.567 23146.297 23438.273 6 JC+R3 11349.557 89 22877.115 22931.605 23228.722 7 JC+R4 11340.087 91 22862.174 22919.516 23221.682 8 JC+R5 11339.948 93 22865.897 22926.187 23233.307 14 F81+F 11927.333 88 24030.666 24083.765 24378.323 15 F81+F+I 11670.259 89 23518.518 23573.008 23870.125 16 F81+F+G4 11358.529 89 22895.058 22949.547 23246.665 17 F81+F+I+G4 11341.895 90 22863.789 22919.694 23219.347 18 F81+F+R2 11457.886 90 23095.773 23151.677 23451.331 19 F81+F+R3 11345.804 92 22875.608 22934.412 23239.067 20 F81+F+R4 11335.393 94 22858.786 22920.585 23230.146 21 F81+F+R5 11335.282 96 22862.564 22927.455 23241.825 27 K2P 11881.076 86 23934.153 23984.537 24273.908 28 K2P+I 11627.075 87 23428.149 23479.879 23771.855 29 K2P+G4 11316.740 87 22807.480 22859.210 23151.186 30 K2P+I+G4 11300.267 88 22776.533 22829.632 23124.190 31 K2P+R2 11416.205 88 23008.409 23061.508 23356.066 32 K2P+R3 11303.971 90 22787.942 22843.846 23143.500 33 K2P+R4 11293.768 92 22771.536 22830.340 23134.995 34 K2P+R5 11293.664 94 22775.327 22837.127 23146.688 40 HKY+F 11884.045 89 23946.090 24000.580 24297.697 41 HKY+F+I 11625.800 90 23431.599 23487.503 23787.157 42 HKY+F+G4 11309.303 90 22798.605 22854.510 23154.163 43 HKY+F+I+G4 11293.017 91 22768.033 22825.376 23127.542 44 HKY+F+R2 11411.536 91 23005.072 23062.415 23364.581 45 HKY+F+R3 11297.610 93 22781.221 22841.510 23148.630 46 HKY+F+R4 11286.412 95 22762.823 22826.157 23138.134 47 HKY+F+R5 11286.351 97 22766.702 22833.178 23149.915 53 TNe 11880.065 87 23934.130 23985.859 24277.835 54 TNe+I 11620.650 88 23417.300 23470.398 23764.956 55 TNe+G4 11315.459 88 22806.918 22860.016 23154.575 56 TNe+I+G4 11298.288 89 22774.575 22829.065 23126.182 57 TNe+R2 11414.812 89 23007.624 23062.114 23359.232 58 TNe+R3 11300.588 91 22783.175 22840.518 23142.684 59 TNe+R4 11290.964 93 22767.928 22828.218 23135.338 60 TNe+R5 11290.801 95 22771.601 22834.935 23146.913 66 TN+F 11882.917 90 23945.834 24001.739 24301.392 67 TN+F+I 11618.509 91 23419.019 23476.361 23778.527 68 TN+F+G4 11307.383 91 22796.766 22854.108 23156.274 69 TN+F+I+G4 11290.263 92 22764.527 22823.331 23127.986 70 TN+F+R2 11409.606 92 23003.211 23062.015 23366.670 71 TN+F+R3 11293.299 94 22774.598 22836.398 23145.959 72 TN+F+R4 11282.625 96 22757.250 22822.142 23136.512 73 TN+F+R5 11282.545 98 22761.089 22829.174 23148.252 79 K3P 11867.490 87 23908.981 23960.711 24252.687 80 K3P+I 11612.745 88 23401.490 23454.588 23749.146 81 K3P+G4 11305.537 88 22787.073 22840.172 23134.730 82 K3P+I+G4 11288.477 89 22754.954 22809.444 23106.561 83 K3P+R2 11401.945 89 22981.891 23036.381 23333.498 84 K3P+R3 11291.942 91 22765.885 22823.227 23125.393 85 K3P+R4 11282.100 93 22750.200 22810.490 23117.610 86 K3P+R5 11282.046 95 22754.092 22817.426 23129.403 92 K3Pu+F 11870.569 90 23921.138 23977.043 24276.696 93 K3Pu+F+I 11611.617 91 23405.233 23462.576 23764.742 94 K3Pu+F+G4 11298.775 91 22779.549 22836.892 23139.058 95 K3Pu+F+I+G4 11281.879 92 22747.758 22806.562 23111.217 96 K3Pu+F+R2 11397.646 92 22979.292 23038.096 23342.751 97 K3Pu+F+R3 11286.226 94 22760.452 22822.251 23131.812 98 K3Pu+F+R4 11275.375 96 22742.751 22807.643 23122.013 99 K3Pu+F+R5 11275.327 98 22746.654 22814.738 23133.817 105 TPM2+F 11883.629 90 23947.257 24003.162 24302.815 106 TPM2+F+I 11625.200 91 23432.400 23489.742 23791.908 107 TPM2+F+G4 11308.868 91 22799.735 22857.078 23159.244 108 TPM2+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 109 TPM2+F+R2 11411.526 92 23007.053 23065.857 23370.512 110 TPM2+F+R3 11297.355 94 22782.711 22844.510 23154.071 111 TPM2+F+R4 11286.270 96 22764.539 22829.431 23143.801 112 TPM2+F+R5 11286.146 98 22768.292 22836.376 23155.455 118 TPM2u+F 11883.629 90 23947.258 24003.162 24302.815 119 TPM2u+F+I 11625.201 91 23432.402 23489.745 23791.911 120 TPM2u+F+G4 11308.867 91 22799.735 22857.077 23159.243 121 TPM2u+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 122 TPM2u+F+R2 11411.527 92 23007.053 23065.857 23370.512 123 TPM2u+F+R3 11297.355 94 22782.710 22844.509 23154.070 124 TPM2u+F+R4 11286.270 96 22764.540 22829.432 23143.802 125 TPM2u+F+R5 11286.143 98 22768.285 22836.370 23155.448 131 TPM3+F 11851.525 90 23883.050 23938.954 24238.608 132 TPM3+F+I 11613.469 91 23408.938 23466.281 23768.447 133 TPM3+F+G4 11305.327 91 22792.654 22849.996 23152.162 134 TPM3+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 135 TPM3+F+R2 11405.175 92 22994.351 23053.155 23357.810 136 TPM3+F+R3 11293.007 94 22774.014 22835.813 23145.374 137 TPM3+F+R4 11283.178 96 22758.356 22823.248 23137.618 138 TPM3+F+R5 11283.049 98 22762.099 22830.183 23149.262 144 TPM3u+F 11851.525 90 23883.050 23938.954 24238.608 145 TPM3u+F+I 11613.469 91 23408.938 23466.281 23768.447 146 TPM3u+F+G4 11305.327 91 22792.655 22849.997 23152.163 147 TPM3u+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 148 TPM3u+F+R2 11405.172 92 22994.345 23053.149 23357.804 149 TPM3u+F+R3 11293.007 94 22774.014 22835.813 23145.374 150 TPM3u+F+R4 11283.172 96 22758.344 22823.236 23137.606 151 TPM3u+F+R5 11283.047 98 22762.095 22830.179 23149.258 157 TIMe 11866.486 88 23908.972 23962.070 24256.629 158 TIMe+I 11606.350 89 23390.699 23445.189 23742.306 159 TIMe+G4 11304.322 89 22786.643 22841.133 23138.250 160 TIMe+I+G4 11286.570 90 22753.139 22809.044 23108.697 161 TIMe+R2 11400.580 90 22981.161 23037.065 23336.718 162 TIMe+R3 11288.530 92 22761.060 22819.864 23124.519 163 TIMe+R4 11279.399 94 22746.797 22808.596 23118.158 164 TIMe+R5 11279.309 96 22750.619 22815.511 23129.880 170 TIM+F 11869.451 91 23920.901 23978.244 24280.410 171 TIM+F+I 11604.362 92 23392.723 23451.527 23756.182 172 TIM+F+G4 11296.948 92 22777.895 22836.699 23141.354 173 TIM+F+I+G4 11279.221 93 22744.442 22804.732 23111.852 174 TIM+F+R2 11395.723 93 22977.446 23037.735 23344.855 175 TIM+F+R3 11281.905 95 22753.810 22817.144 23129.121 176 TIM+F+R4 11271.730 97 22737.460 22803.935 23120.672 177 TIM+F+R5 11271.695 99 22741.389 22811.107 23132.503 183 TIM2e 11879.551 88 23935.102 23988.200 24282.758 184 TIM2e+I 11619.949 89 23417.898 23472.388 23769.506 185 TIM2e+G4 11315.204 89 22808.409 22862.898 23160.016 186 TIM2e+I+G4 11298.141 90 22776.282 22832.187 23131.840 187 TIM2e+R2 11414.742 90 23009.484 23065.388 23365.041 188 TIM2e+R3 11300.473 92 22784.945 22843.750 23148.405 189 TIM2e+R4 11290.833 94 22769.667 22831.466 23141.027 190 TIM2e+R5 11290.739 96 22773.478 22838.370 23152.740 196 TIM2+F 11882.506 91 23947.012 24004.354 24306.520 197 TIM2+F+I 11617.928 92 23419.855 23478.659 23783.314 198 TIM2+F+G4 11306.963 92 22797.925 22856.729 23161.384 199 TIM2+F+I+G4 11289.986 93 22765.972 22826.262 23133.382 200 TIM2+F+R2 11409.581 93 23005.161 23065.451 23372.571 201 TIM2+F+R3 11293.076 95 22776.151 22839.485 23151.462 202 TIM2+F+R4 11282.473 97 22758.946 22825.422 23142.159 203 TIM2+F+R5 11282.402 99 22762.805 22832.523 23153.918 209 TIM3e 11838.747 88 23853.494 23906.592 24201.150 210 TIM3e+I 11602.540 89 23383.080 23437.570 23734.687 211 TIM3e+G4 11307.306 89 22792.612 22847.102 23144.219 212 TIM3e+I+G4 11291.340 90 22762.680 22818.585 23118.238 213 TIM3e+R2 11403.257 90 22986.514 23042.418 23342.071 214 TIM3e+R3 11291.597 92 22767.193 22825.997 23130.652 215 TIM3e+R4 11283.522 94 22755.045 22816.844 23126.405 216 TIM3e+R5 11283.418 96 22758.835 22823.727 23138.097 222 TIM3+F 11850.147 91 23882.293 23939.636 24241.802 223 TIM3+F+I 11606.170 92 23396.339 23455.144 23759.799 224 TIM3+F+G4 11303.297 92 22790.593 22849.397 23154.052 225 TIM3+F+I+G4 11287.023 93 22760.046 22820.336 23127.456 226 TIM3+F+R2 11403.216 93 22992.433 23052.722 23359.842 227 TIM3+F+R3 11288.650 95 22767.299 22830.632 23142.610 228 TIM3+F+R4 11279.141 97 22752.282 22818.757 23135.494 229 TIM3+F+R5 11279.094 99 22756.187 22825.905 23147.301 235 TVMe 11826.121 89 23830.242 23884.732 24181.849 236 TVMe+I 11594.361 90 23368.722 23424.627 23724.280 237 TVMe+G4 11295.606 90 22771.211 22827.116 23126.769 238 TVMe+I+G4 11280.065 91 22742.130 22799.473 23101.639 239 TVMe+R2 11390.331 91 22962.661 23020.004 23322.170 240 TVMe+R3 11281.356 93 22748.713 22809.003 23116.123 241 TVMe+R4 11273.798 95 22737.595 22800.929 23112.906 242 TVMe+R5 11273.698 97 22741.396 22807.871 23124.608 248 TVM+F 11837.769 92 23859.537 23918.341 24222.996 249 TVM+F+I 11599.049 93 23384.097 23444.387 23751.507 250 TVM+F+G4 11292.632 93 22771.264 22831.554 23138.674 251 TVM+F+I+G4 11276.861 94 22741.721 22803.521 23113.082 252 TVM+F+R2 11390.890 94 22969.780 23031.579 23341.140 253 TVM+F+R3 11279.704 96 22751.409 22816.301 23130.671 254 TVM+F+R4 11270.720 98 22737.439 22805.524 23124.602 255 TVM+F+R5 11270.590 100 22741.181 22812.559 23136.245 261 SYM 11824.854 90 23829.707 23885.612 24185.265 262 SYM+I 11587.951 91 23357.902 23415.245 23717.411 263 SYM+G4 11294.178 91 22770.357 22827.699 23129.865 264 SYM+I+G4 11278.013 92 22740.027 22798.831 23103.486 265 SYM+R2 11388.873 92 22961.746 23020.550 23325.205 266 SYM+R3 11277.825 94 22743.649 22805.449 23115.010 267 SYM+R4 11270.756 96 22733.511 22798.403 23112.773 268 SYM+R5 11270.608 98 22737.216 22805.300 23124.379 274 GTR+F 11836.396 93 23858.792 23919.082 24226.202 275 GTR+F+I 11591.768 94 23371.536 23433.336 23742.897 276 GTR+F+G4 11290.699 94 22769.397 22831.197 23140.758 277 GTR+F+I+G4 11274.183 95 22738.365 22801.698 23113.676 278 GTR+F+R2 11389.047 95 22968.093 23031.427 23343.404 279 GTR+F+R3 11275.377 97 22744.753 22811.229 23127.966 280 GTR+F+R4 11266.912 99 22731.824 22801.543 23122.938 281 GTR+F+R5 11266.818 101 22735.637 22808.701 23134.652 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+R4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 0.076 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.077 seconds (0h:0m:0s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.956 / LogL: -11295.603 Init pinv, alpha: 0.012, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.077 Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.570 / LogL: -11280.070 Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.568 / LogL: -11280.070 Init pinv, alpha: 0.046, 1.000 / Estimate: 0.085, 1.571 / LogL: -11280.067 Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.569 / LogL: -11280.068 Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.065 Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.575 / LogL: -11280.064 Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.064 Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.065 Optimal pinv,alpha: 0.085, 1.575 / LogL: -11280.064 Parameters optimization took 2.418 sec Computing ML distances based on estimated model parameters... 0.025 sec Computing BIONJ tree... 0.002 seconds Log-likelihood of BIONJ tree: -11256.375 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.949 second Computing log-likelihood of 98 initial trees ... 2.779 seconds Current best score: -11230.916 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11225.741 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 9: -11225.461 Iteration 10 / LogL: -11227.958 / Time: 0h:0m:8s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 15: -11224.864 Iteration 20 / LogL: -11231.326 / Time: 0h:0m:10s Finish initializing candidate tree set (14) Current best tree score: -11224.864 / CPU time: 8.071 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11225.318 / Time: 0h:0m:14s (0h:0m:41s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 40: -11222.801 Iteration 40 / LogL: -11222.801 / Time: 0h:0m:17s (0h:0m:44s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 48: -11222.783 Iteration 50 / LogL: -11223.657 / Time: 0h:0m:20s (0h:0m:40s left) Iteration 60 / LogL: -11223.455 / Time: 0h:0m:22s (0h:0m:34s left) Iteration 70 / LogL: -11222.830 / Time: 0h:0m:25s (0h:0m:28s left) Iteration 80 / LogL: -11222.805 / Time: 0h:0m:28s (0h:0m:24s left) Iteration 90 / LogL: -11222.784 / Time: 0h:0m:30s (0h:0m:20s left) Iteration 100 / LogL: -11223.065 / Time: 0h:0m:33s (0h:0m:16s left) Iteration 110 / LogL: -11231.740 / Time: 0h:0m:36s (0h:0m:12s left) Iteration 120 / LogL: -11225.027 / Time: 0h:0m:38s (0h:0m:9s left) Iteration 130 / LogL: -11223.056 / Time: 0h:0m:41s (0h:0m:5s left) Iteration 140 / LogL: -11222.937 / Time: 0h:0m:44s (0h:0m:2s left) TREE SEARCH COMPLETED AFTER 149 ITERATIONS / Time: 0h:0m:47s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.783 Optimal log-likelihood: -11222.780 Rate parameters: A-C: 1.50033 A-G: 2.57814 A-T: 1.65222 C-G: 1.95798 C-T: 2.57814 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.529 Parameters optimization took 1 rounds (0.044 sec) BEST SCORE FOUND : -11222.780 Total tree length: 12.601 Total number of iterations: 149 CPU time used for tree search: 86.715 sec (0h:1m:26s) Wall-clock time used for tree search: 44.720 sec (0h:0m:44s) Total CPU time used: 91.765 sec (0h:1m:31s) Total wall-clock time used: 47.297 sec (0h:0m:47s) 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: Fri Aug 5 07:44:51 2022 91.87user 0.88system 0:47.41elapsed 195%CPU (0avgtext+0avgdata 13940maxresident)k 0inputs+0outputs (0major+1291minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.aErHl0 190.97user 1.53system 2:30.05elapsed 128%CPU (0avgtext+0avgdata 14660maxresident)k 0inputs+0outputs (0major+5834minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_install -Bbuild.omp cd build.omp && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make 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make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/sprng /build/iqtree-1.6.9+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.omp 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make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 50%] Built target whtest [ 55%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 64%] Built target pda make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= [ 68%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/tree /build/iqtree-1.6.9+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 98%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' dh_auto_install -Bbuild.serial cd build.serial && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 3%] Built target lbfgsb [ 3%] Built target vectorclass [ 7%] Built target gsl make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend [ 8%] Built target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 15%] Built target nclextra [ 25%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= [ 41%] Built target pll make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 42%] Built target kernelsse [ 43%] Built target kernelavx make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build [ 44%] Built target kernelfma make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 50%] Built target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 55%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 64%] Built target pda [ 68%] Built target alignment make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/model /build/iqtree-1.6.9+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/tree /build/iqtree-1.6.9+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' dh_auto_install -Bbuild.mpi cd build.mpi && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/mympi.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/gsl /build/iqtree-1.6.9+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/ncl /build/iqtree-1.6.9+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build [ 1%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend [ 2%] Built target vectorclass make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 6%] Built target gsl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build [ 10%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 11%] Built target pllavx [ 14%] Built target nclextra make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build [ 24%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/alignment /build/iqtree-1.6.9+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 25%] Built target kernelavx [ 26%] Built target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 27%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/mympi.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 28%] Built target mympi make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 43%] Built target pll make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build [ 49%] Built target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 54%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 63%] Built target pda make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/model /build/iqtree-1.6.9+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= [ 67%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/tree /build/iqtree-1.6.9+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi" to "" -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_install find debian -name iqtree-mpi -exec chrpath --delete \{\} \; find debian -name iqtree-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' mkdir -p /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-omp > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree-mpi.1 make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'iqtree' in '../iqtree_1.6.9+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_1.6.9+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iqtree_1.6.9+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) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/39253 and its subdirectories I: Current time: Fri Aug 5 07:46:02 -12 2022 I: pbuilder-time-stamp: 1659728762