Diff of the two buildlogs: -- --- b1/build.log 2023-04-25 02:42:54.283651042 +0000 +++ b2/build.log 2023-04-25 03:05:00.060889969 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 26 20:21:41 -12 2024 -I: pbuilder-time-stamp: 1716798101 +I: Current time: Tue Apr 25 16:42:58 +14 2023 +I: pbuilder-time-stamp: 1682390578 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./iqtree_2.0.7+dfsg.orig.tar.xz] I: copying [./iqtree_2.0.7+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Jan 21 02:08:08 2022 -12 +gpgv: Signature made Sat Jan 22 04:08:08 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -26,135 +26,167 @@ dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2789017/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 25 16:43 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/446769/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='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4477be8833ac4b5caec5400176e1422d' - 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='2789017' - PS1='# ' - PS2='> ' + INVOCATION_ID=65c472d7c0a54ba49ad29c9e856292f9 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=446769 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/r-b-build.aPoyGWrE/pbuilderrc_efrB --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b1 --logfile b1/build.log iqtree_2.0.7+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/pbuilderrc_v8O6 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b2 --logfile b2/build.log --extrapackages usrmerge iqtree_2.0.7+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2789017/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 25 16:43 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -324,7 +356,7 @@ Get: 114 http://deb.debian.org/debian bookworm/main amd64 libsprng2-dev amd64 2.0a-13 [77.9 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get: 116 http://deb.debian.org/debian bookworm/main amd64 time amd64 1.9-0.2 [50.8 kB] -Fetched 71.1 MB in 2s (37.6 MB/s) +Fetched 71.1 MB in 3s (25.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19596 files and directories currently installed.) @@ -806,8 +838,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1030,168 +1073,183 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' dh_auto_build -Bbuild.omp - cd build.omp && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.omp && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/terraphast /build/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/ncl /build/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build -[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/terraphast /build/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/ncl /build/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/sprng /build/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/gsl /build/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/booster /build/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/nclextra /build/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -[ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/whtest /build/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -[ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -[ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build +[ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build +[ 1%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +[ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c -[ 5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c -[ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +[ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp -[ 6%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: -/build/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' - 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); - | ^~~~~~~~~~~~~~~~~~ -[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp -[ 8%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +[ 2%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c -In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +[ 3%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +[ 4%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp +cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c +[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp +[ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp +[ 6%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 8%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c -[ 8%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +[ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c -[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp -[ 9%] Linking CXX static library libvectorclass.a +[ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +[ 7%] Linking CXX static library libvectorclass.a +cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 10%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.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-2.0.7+dfsg/build.omp' -[ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp -[ 10%] Built target vectorclass -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c +[ 7%] Built target vectorclass +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/nclextra /build/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -[ 10%] Building C object booster/CMakeFiles/booster.dir/io.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +[ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 10%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c -[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -[ 11%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp -[ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp +[ 8%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +[ 8%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 8%] Building C object booster/CMakeFiles/booster.dir/io.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: +/build/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' + 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); + | ^~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp +[ 11%] Linking C static library libsprng.a +cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +[ 12%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +/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 +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c +/usr/bin/ranlib libsprng.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 12%] Built target sprng +[ 13%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c +[ 13%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1207,84 +1265,100 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 13%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c -[ 13%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c -[ 13%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c -[ 13%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 13%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: +[ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp +[ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' - 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' - 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' - 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' - 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); - | ^~~~~~~~~~~~~~~~~~ -[ 14%] Linking C static library libsprng.a -cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o -[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +[ 14%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c +[ 15%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c +[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp -/usr/bin/ranlib libsprng.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 15%] Built target sprng -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/whtest /build/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp -[ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c -[ 15%] Linking CXX static library libgsl.a +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 16%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 16%] Linking CXX static library libgsl.a cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 15%] Built target gsl -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -[ 15%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +[ 16%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c +[ 16%] Built target gsl +[ 17%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c +[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1298,44 +1372,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 16%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c -[ 16%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c -/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' - 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' - 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); - | ^~~~~~~~~~~~~~~~~~ -[ 18%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c -[ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp -[ 18%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c +[ 17%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1345,39 +1397,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 20%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c -In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: -/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' - 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' - 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -[ 21%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +[ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp +[ 19%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c -[ 21%] Building C object pll/CMakeFiles/pll.dir/models.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c -[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp -[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +[ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o /build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); @@ -1392,141 +1416,129 @@ /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 19%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c +[ 19%] Linking CXX static library liblbfgsb.a In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 22%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c -[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c -[ 22%] Linking CXX static library liblbfgsb.a cd /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 22%] Built target lbfgsb +[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +[ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +[ 19%] Built target lbfgsb +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' + 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' + 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' + 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' + 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); + | ^~~~~~~~~~~~~~~~~~ make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +[ 19%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp -[ 23%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c -[ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c -[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c -[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -[ 28%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp -[ 29%] Linking C static library libbooster.a -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a +[ 19%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c +[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp +[ 21%] Linking C static library libpllavx.a +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 29%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -[ 29%] Built target booster +[ 21%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/utils /build/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 29%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +[ 21%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -[ 30%] Linking C static library libpllavx.a -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp -[ 31%] Built target pllavx -[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c +In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' + 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' + 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); + | ^~~~~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1540,16 +1552,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ +[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp +[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 25%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: @@ -1566,8 +1576,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp +[ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: @@ -1585,45 +1595,106 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +[ 26%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c +/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 27%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c +[ 28%] Linking CXX static library libwhtest.a +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +/usr/bin/ranlib libwhtest.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 28%] Built target whtest +[ 28%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c +[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp -[ 33%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c -In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: +[ 29%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c +[ 29%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c -In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: +/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' + 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' + 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +[ 31%] Linking C static library libbooster.a +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +/usr/bin/ranlib libbooster.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 31%] Built target booster +[ 31%] Building C object pll/CMakeFiles/pll.dir/models.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c +[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp +[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1631,15 +1702,36 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 34%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 32%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp +[ 32%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 32%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c +In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +[ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c +[ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c +In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1656,135 +1748,195 @@ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ +[ 35%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp -[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp -[ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +[ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c -[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp -[ 36%] Linking CXX static library libterraphast.a -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o -[ 37%] Linking CXX static library libwhtest.a -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -/usr/bin/ranlib libterraphast.a -cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp +[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 40%] Linking CXX static library libnclextra.a +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +[ 40%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp +[ 40%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c +/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-2.0.7+dfsg/build.omp' -/usr/bin/ranlib libwhtest.a In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 37%] Built target terraphast -[ 37%] Built target whtest -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -[ 38%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 38%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +[ 40%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pda /build/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 40%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +[ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c -[ 39%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp -[ 40%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +[ 41%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c -[ 40%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp -[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp +[ 42%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp -[ 41%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +[ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c -[ 42%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ [ 43%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c -In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: +In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 43%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c -[ 43%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 43%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c +[ 43%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c +[ 44%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 45%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c +[ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c +In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 45%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: @@ -1797,40 +1949,18 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 44%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c -[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp -[ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp -[ 46%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c -In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp -[ 47%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 45%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c +[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1892,101 +2022,43 @@ /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp -[ 48%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/map:60, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp -[ 49%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp -[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp -[ 51%] Linking C static library libpll.a -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp -/usr/bin/ranlib libpll.a +[ 46%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp +[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp +[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 47%] Linking CXX static library libterraphast.a +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +/usr/bin/ranlib libterraphast.a +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 51%] Built target pll -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 48%] Built target terraphast +[ 48%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp -[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp -[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2000,14 +2072,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2021,44 +2089,44 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 56%] Linking CXX static library libnclextra.a -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -/usr/bin/ranlib libnclextra.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 56%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pda /build/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +[ 49%] Linking C static library libpll.a +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a +[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +[ 49%] Built target pll +[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +[ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/map:60, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +[ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp +[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2072,27 +2140,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 58%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp -[ 58%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2108,41 +2155,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 59%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2156,8 +2172,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 59%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2174,22 +2188,31 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +[ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp +[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2203,12 +2226,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2222,8 +2243,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp +[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2239,12 +2262,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE 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-fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: @@ -2261,12 +2282,28 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp -[ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp +[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +[ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp +[ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp +[ 61%] Linking CXX static library libncl.a +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, @@ -2274,33 +2311,44 @@ /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Linking CXX static library libyaml-cpp.a -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp +/usr/bin/ranlib libncl.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 61%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/alignment /build/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libyaml-cpp.a +[ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2316,49 +2364,62 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 64%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/pda/split.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= -[ 64%] Linking CXX static library libutils.a -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -[ 64%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp -/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-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Built target utils In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/split.h:25: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Linking CXX static library libutils.a +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 +/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o +/usr/bin/ranlib libutils.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c +[ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/model /build/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= @@ -2366,6 +2427,32 @@ make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, @@ -2379,12 +2466,26 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp +[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2403,31 +2504,43 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp -[ 67%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp -[ 67%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp -[ 67%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 68%] Linking CXX static library libyaml-cpp.a +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2443,12 +2556,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libyaml-cpp.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 68%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2458,12 +2580,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2473,48 +2597,127 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 67%] Linking CXX static library libncl.a -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o +/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2524,20 +2727,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libncl.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 67%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend -[ 68%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/alignment /build/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2547,59 +2751,17 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: -/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: -/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -2613,29 +2775,31 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -[ 68%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp -/build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 242 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2644,8 +2808,8 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2655,15 +2819,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2673,10 +2834,26 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 242 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2695,22 +2872,8 @@ /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ -[ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2723,6 +2886,48 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: +/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: +/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 72%] Linking CXX static library libpda.a +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +/usr/bin/ranlib libpda.a +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 73%] Built target pda +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/main /build/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 74%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2758,6 +2963,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2772,27 +2982,23 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 70%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +[ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp +In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2805,19 +3011,7 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2830,23 +3024,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2881,7 +3060,8 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2891,75 +3071,35 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 72%] Linking CXX static library libpda.a -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 72%] Built target pda -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/main /build/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 73%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp -/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ -[ 75%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp -[ 75%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Linking CXX static library libphyloYAML.a cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -[ 77%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +/usr/bin/ranlib libphyloYAML.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 76%] Built target phyloYAML +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: + from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' -[ 77%] Built target phyloYAML +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2974,10 +3114,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 77%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o -[ 77%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -2992,8 +3132,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3008,17 +3148,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp -[ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, - from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3028,16 +3162,15 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - | ^~~~~ +[ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, + from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3051,7 +3184,9 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, + from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3061,6 +3196,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3077,12 +3228,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3092,8 +3245,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3106,29 +3260,20 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3150,56 +3295,12 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: -/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: -/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3216,10 +3317,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp -[ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp +[ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3227,8 +3326,7 @@ from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: + from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3238,10 +3336,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 81%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -[ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3249,7 +3359,8 @@ from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3274,59 +3385,45 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: +/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: +/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3356,8 +3453,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3373,6 +3468,8 @@ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3396,21 +3493,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -3432,41 +3530,6 @@ /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3479,26 +3542,6 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp -[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp -[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, @@ -3567,20 +3610,20 @@ /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 84%] Built target kernelsse -[ 84%] Linking CXX static library libkernelavx.a -/usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake [ 85%] 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/kernelavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /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 libkernelavx.a /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' +[ 85%] Built target kernelfma +[ 85%] 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-2.0.7+dfsg/build.omp' [ 85%] Built target kernelavx -[ 85%] Built target kernelfma [ 86%] Linking CXX static library libmain.a cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 @@ -3612,39 +3655,37 @@ [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3658,22 +3699,21 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3685,8 +3725,9 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3699,8 +3740,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3726,16 +3767,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, + from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3745,17 +3778,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3770,8 +3795,7 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3783,27 +3807,34 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, - from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3812,9 +3843,7 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3827,20 +3856,25 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3850,17 +3884,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3870,26 +3897,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -3903,12 +3914,32 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: @@ -3921,13 +3952,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3953,13 +3982,11 @@ | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3969,18 +3996,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] - 653 | } - | ^ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] - 1298 | } - | ^ -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3993,6 +4010,10 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, @@ -4007,19 +4028,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -4036,6 +4044,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -4051,6 +4073,27 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] + 653 | } + | ^ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] + 1298 | } + | ^ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -4137,7 +4180,7 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial - cd build.serial && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.serial && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks @@ -4145,130 +4188,96 @@ make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/booster /build/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/gsl /build/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/terraphast /build/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/ncl /build/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/nclextra /build/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/whtest /build/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/sprng /build/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/sprng /build/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp +[ 0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/gsl /build/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +[ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp -[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -[ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +[ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +[ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o +[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build -[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +[ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -[ 5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +[ 4%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c -[ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp -[ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -[ 6%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -[ 6%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp +[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -4280,35 +4289,18 @@ /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +[ 6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c -[ 7%] Linking CXX static library libvectorclass.a -cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c -cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 7%] Built target vectorclass -[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +[ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c -[ 7%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp -[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +[ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 8%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c -In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 8%] Building C object booster/CMakeFiles/booster.dir/io.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -4338,22 +4330,32 @@ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -[ 9%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c -[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp -[ 10%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' + 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' + 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); + | ^~~~~~~~~~~~~~~~~~ +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c -[ 10%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c -[ 11%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -[ 11%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4367,22 +4369,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 12%] Linking C static library libsprng.a -cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -/usr/bin/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-2.0.7+dfsg/build.serial' -[ 12%] Built target sprng -[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 10%] Linking C static library libsprng.a +cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4396,11 +4390,35 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp +cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o +/usr/bin/ranlib libsprng.a +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 10%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c +[ 10%] Built target sprng +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/booster /build/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 11%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4414,68 +4432,39 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 14%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c -[ 14%] Linking CXX static library libgsl.a +[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp +[ 13%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c +[ 13%] Linking CXX static library libgsl.a cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -[ 14%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c +[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp +[ 14%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.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 -/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 15%] Built target gsl -In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' - 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' - 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); - | ^~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 17%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 17%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c -[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp -[ 18%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 14%] Built target gsl +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +[ 14%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 15%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c -[ 18%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 15%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c +[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +[ 16%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -4493,61 +4482,43 @@ /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: +In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 19%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c -[ 19%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c -[ 20%] Building C object booster/CMakeFiles/booster.dir/booster.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c -[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 20%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c -/build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': -/build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); - | ^~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: -/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -/build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { - | ^~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: +[ 16%] Building C object booster/CMakeFiles/booster.dir/io.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c +In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 17%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c +[ 17%] Linking CXX static library libvectorclass.a +cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 17%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c +[ 17%] Built target vectorclass +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/nclextra /build/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp +[ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 20%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4557,20 +4528,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 21%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +[ 19%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c -[ 21%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c -[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp -[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp -[ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4583,9 +4548,6 @@ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -4598,50 +4560,8 @@ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -[ 22%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/utils /build/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c -[ 22%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -[ 23%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c -[ 24%] Linking C static library libpllavx.a -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 24%] Built target pllavx -[ 24%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c -[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp -[ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -[ 26%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c -[ 27%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4655,21 +4575,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp -[ 27%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4677,49 +4587,56 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp -[ 29%] Linking C static library libbooster.a -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp -[ 30%] Built target booster -[ 30%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp +[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +[ 21%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 22%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4733,31 +4650,70 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c +/build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': +/build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); + | ^~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: +/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +/build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { + | ^~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +[ 22%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 22%] Built target lbfgsb +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/whtest /build/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 22%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 23%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c +In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 23%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c +[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp +[ 23%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c +[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +[ 25%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4771,72 +4727,124 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp -[ 31%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +[ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 26%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c +In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 26%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp +[ 28%] Linking C static library libbooster.a +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +[ 28%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -[ 32%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +/usr/bin/ranlib libbooster.a +[ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 30%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c -[ 32%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c -[ 33%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp +[ 30%] Built target booster +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +[ 30%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 30%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 30%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c +[ 31%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 34%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 34%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +[ 31%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 31%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c -[ 34%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp -[ 34%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp -[ 35%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c +[ 32%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c -[ 35%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c +[ 33%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c -[ 36%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c +[ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 37%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp -[ 37%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: + from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4844,28 +4852,28 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 38%] Linking CXX static library libnclextra.a -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -[ 38%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +[ 34%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c +In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 34%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 34%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/usr/bin/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-2.0.7+dfsg/build.serial' -[ 38%] Built target nclextra -[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 35%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -4927,56 +4935,62 @@ /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp -[ 40%] Linking CXX static library libwhtest.a -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 41%] Built target whtest -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pda /build/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 41%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp +[ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp +[ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 38%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 41%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: + from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp +[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4990,60 +5004,58 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 41%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp -[ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 40%] Linking C static library libpll.a +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 40%] Built target pll +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, - from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 44%] Linking C static library libpll.a -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -/usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 45%] Built target pll -[ 45%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5057,43 +5069,47 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp -[ 46%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +[ 41%] Linking C static library libpllavx.a +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 41%] Built target pllavx +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/utils /build/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +[ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 42%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp +[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: + from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/map:60, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5107,9 +5123,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: + from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5117,30 +5135,21 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp -[ 48%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp -[ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp -[ 48%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp -[ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp -[ 49%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp +[ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp +[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5154,85 +5163,185 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +[ 46%] Linking CXX static library libwhtest.a +cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P 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-I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +[ 49%] Linking CXX static library libnclextra.a +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +/usr/bin/ranlib libnclextra.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 49%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pda /build/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp +[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, - from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +[ 52%] Linking CXX static library libterraphast.a +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +[ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp +/usr/bin/ranlib libterraphast.a +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 54%] Built target terraphast +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 54%] Linking CXX static library libncl.a +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o +/usr/bin/ranlib libncl.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 54%] Built target ncl +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp -[ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp -[ 52%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 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CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp +[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp +[ 57%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 57%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp +[ 58%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp +[ 58%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp +[ 58%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/alignment /build/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp -[ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp -[ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 59%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pruning.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, + from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5242,52 +5351,35 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp -[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp -[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp -[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5296,25 +5388,16 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/12/sstream:38, + from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp -[ 58%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp -[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp -[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -[ 59%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5322,180 +5405,129 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 61%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/map:60, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/split.h:25: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, + from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp +[ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 59%] Linking CXX static library libterraphast.a -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 -[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o -/usr/bin/ranlib libterraphast.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 59%] Built target terraphast -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pruning.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +[ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp -[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp -[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp -[ 61%] Linking CXX static library libutils.a -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o -/usr/bin/ranlib libutils.a +[ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: + from /build/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 61%] Built target utils -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/model /build/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, - from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp -[ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp -[ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp -[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5503,12 +5535,30 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 65%] Linking CXX static library libyaml-cpp.a +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" +/usr/bin/ranlib libyaml-cpp.a +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 65%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 65%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -5527,76 +5577,80 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp -[ 66%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp -[ 66%] Linking CXX static library libncl.a -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -[ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, + from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -/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 In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libncl.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 66%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/alignment /build/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5606,21 +5660,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -5628,26 +5680,24 @@ from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5657,78 +5707,17 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 242 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: -/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: -/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -[ 68%] Linking CXX static library libyaml-cpp.a -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" -[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp -/usr/bin/ranlib libyaml-cpp.a +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5743,26 +5732,37 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + | ^~~~~ +[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5772,34 +5772,61 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 69%] Linking CXX static library libutils.a +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 +/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o +/usr/bin/ranlib libutils.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 69%] Built target utils +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/model /build/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -5807,47 +5834,65 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: +/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: +/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5873,22 +5918,74 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp -[ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 242 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp +[ 72%] Linking CXX static library libpda.a +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +/usr/bin/ranlib libpda.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 72%] Built target pda +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' +cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/main /build/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake --color= /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -5904,9 +6001,14 @@ /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ +[ 73%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -5919,62 +6021,12 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, @@ -6009,15 +6061,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: + from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6027,16 +6075,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: + from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6046,25 +6089,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp -[ 74%] Linking CXX static library libpda.a -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 75%] Linking CXX static library libphyloYAML.a +cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 +/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o +/usr/bin/ranlib libphyloYAML.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 75%] Built target phyloYAML +[ 75%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp +[ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp +/build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ +[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -6078,40 +6118,15 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 74%] Built target pda -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/main /build/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 75%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp -/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ +[ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6121,16 +6136,24 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 75%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -/build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: + from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6140,13 +6163,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: + from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6156,17 +6177,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6176,8 +6192,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -6195,6 +6223,8 @@ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); @@ -6203,6 +6233,28 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function @@ -6241,21 +6293,26 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp -[ 79%] Linking CXX static library libphyloYAML.a -cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 -/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 79%] Built target phyloYAML [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: @@ -6288,7 +6345,9 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, + from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6298,13 +6357,15 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, - from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelcodon.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6314,13 +6375,15 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelcodon.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6330,12 +6393,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6348,37 +6405,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, @@ -6386,8 +6414,7 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelunrest.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6401,10 +6428,6 @@ cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp -[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6423,6 +6446,24 @@ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelunrest.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6447,32 +6488,6 @@ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -6480,8 +6495,7 @@ from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: + from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6498,7 +6512,8 @@ from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6508,6 +6523,18 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -6524,46 +6551,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp -[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, - from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /usr/include/c++/12/complex:45, - from /usr/include/eigen3/Eigen/Core:50, - from /usr/include/eigen3/Eigen/Dense:1, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6579,7 +6570,7 @@ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6592,14 +6583,31 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: -/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /usr/include/c++/12/complex:45, + from /usr/include/eigen3/Eigen/Core:50, + from /usr/include/eigen3/Eigen/Dense:1, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6612,26 +6620,36 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: -/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, + from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -6659,6 +6677,31 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +/build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } @@ -6688,6 +6731,13 @@ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 85%] Built target kernelavx +[ 85%] Linking CXX static library libalignment.a +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 +/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +/usr/bin/ranlib libalignment.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' +[ 85%] Built target alignment [ 86%] Linking CXX static library libmain.a cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 @@ -6695,13 +6745,6 @@ /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 86%] Built target main -[ 86%] Linking CXX static library libalignment.a -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 -/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -/usr/bin/ranlib libalignment.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' -[ 86%] Built target alignment [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -6717,69 +6760,71 @@ make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6791,8 +6836,7 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6805,8 +6849,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6818,23 +6862,24 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, - from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6847,23 +6892,21 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6875,7 +6918,9 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6891,8 +6936,7 @@ from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6904,8 +6948,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6918,41 +6962,22 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, + from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6967,7 +6992,9 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6977,20 +7004,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -7004,6 +7017,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o @@ -7012,29 +7027,11 @@ cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7060,19 +7057,13 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] - 653 | } - | ^ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] - 1298 | } - | ^ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7082,15 +7073,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/supernode.h:23, - from /build/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7104,8 +7105,7 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/tinatree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7115,8 +7115,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -7129,6 +7131,55 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/supernode.h:23, + from /build/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/tinatree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/parstree.h:11, + from /build/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -7158,22 +7209,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/parstree.h:11, - from /build/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] + 653 | } + | ^ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] + 1298 | } + | ^ [ 98%] Linking CXX static library libtree.a cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -7244,181 +7287,100 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi - cd build.mpi && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.mpi && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/booster /build/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/ncl /build/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/gsl /build/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/whtest /build/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pll 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make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/sprng /build/iqtree-2.0.7+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -make[4]: Leaving directory 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-I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 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CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra 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-I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp +[ 3%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c +[ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp -[ 4%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -[ 5%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -[ 5%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c -[ 5%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 5%] Building C object booster/CMakeFiles/booster.dir/io.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c -[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp -[ 6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c -[ 7%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c -[ 7%] Linking CXX static library libvectorclass.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 7%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c -cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -[ 8%] Building C object booster/CMakeFiles/booster.dir/booster.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 8%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -[ 8%] Built target vectorclass -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c -[ 9%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -/build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': -/build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); - | ^~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: -/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -/build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { - | ^~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -[ 10%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c -[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -[ 12%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -7430,138 +7392,10 @@ /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 12%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c -[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp -[ 12%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -[ 12%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 12%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c -[ 12%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c -[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 13%] Linking C static library libsprng.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o -/usr/bin/ranlib libsprng.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 13%] Built target sprng -[ 14%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 14%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c -[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp -[ 16%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c -[ 16%] Linking CXX static library libgsl.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake 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yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp -/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-2.0.7+dfsg/build.mpi' -[ 16%] Built target gsl -[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 18%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c -[ 19%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp -[ 21%] Linking C static library libbooster.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -[ 21%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 21%] Built target booster -[ 21%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c -[ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -7591,6 +7425,22 @@ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ +[ 5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c +[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c +[ 6%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c +[ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c +[ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c +/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -7607,98 +7457,58 @@ /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp -[ 24%] Linking C static library libpllavx.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a +[ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp +[ 8%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c +[ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c +[ 9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c +[ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c +[ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c +[ 11%] Linking C static library libsprng.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o +/usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 24%] Built target pllavx -[ 24%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp -[ 24%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c -[ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +[ 11%] Built target sprng +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend +[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/booster /build/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c -[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -[ 26%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c -[ 26%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 27%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c -[ 27%] Built target lbfgsb -[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp -[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp -[ 27%] Building C object pll/CMakeFiles/pll.dir/models.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7712,19 +7522,10 @@ /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp -[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +[ 12%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7738,83 +7539,79 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp -[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp -[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp +[ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -[ 32%] Linking CXX static library libwhtest.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 32%] Built target whtest -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/utils /build/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 32%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp -[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp -[ 34%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +[ 14%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +[ 14%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c +[ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 35%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +[ 15%] Linking CXX static library libgsl.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 15%] Built target gsl +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +[ 16%] Building C object booster/CMakeFiles/booster.dir/io.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c +[ 17%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 18%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c +[ 18%] Linking CXX static library libvectorclass.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 18%] Built target vectorclass +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +[ 18%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7827,14 +7624,8 @@ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': -/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ +[ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -7847,9 +7638,18 @@ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ +[ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c +In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: + from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7857,38 +7657,57 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp -[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -[ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -[ 37%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c -[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp -In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: -/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': +/build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +[ 21%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7902,71 +7721,79 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp -[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp -[ 41%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c -[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 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-MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp -[ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion 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-MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -[ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -[ 43%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp -[ 43%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 21%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +[ 21%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp -[ 44%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp -[ 45%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 22%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 45%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +[ 23%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c +[ 23%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 23%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c -[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp -[ 47%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c +[ 23%] Built target lbfgsb +/build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': +/build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); + | ^~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: +/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +/build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { + | ^~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/whtest /build/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 23%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c +[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp +[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +[ 25%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c +[ 25%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c +[ 25%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7980,53 +7807,69 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 48%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 48%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 25%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c +[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 26%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c +[ 27%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c +[ 27%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c -[ 49%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 28%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: +In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: +[ 29%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c +In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 49%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp +[ 30%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp -[ 49%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 31%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c -[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp +[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +[ 31%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -8088,57 +7931,34 @@ /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp -[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp -[ 51%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp -[ 51%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp -[ 52%] Linking CXX static library libnclextra.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -/usr/bin/ranlib libnclextra.a +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c +[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +[ 32%] Linking C static library libbooster.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +/usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 52%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +[ 32%] Built target booster +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pda /build/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp -[ 52%] Linking CXX static library libterraphast.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o -/usr/bin/ranlib libterraphast.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 52%] Built target terraphast -[ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 32%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +[ 33%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp +[ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c +[ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8152,63 +7972,96 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Linking C static library libpll.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +[ 37%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c +In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: +/build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp +[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +[ 39%] Linking C static library libpll.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 54%] Built target pll -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +[ 39%] Built target pll +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8222,23 +8075,16 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 39%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp +[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, - from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8253,7 +8099,8 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8267,31 +8114,36 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp -[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp +[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp +[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/map:60, - from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp -[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp -[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8305,8 +8157,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8320,12 +8174,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp -[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +[ 44%] Linking C static library libpllavx.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 44%] Built target pllavx +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/utils /build/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8339,8 +8202,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp +[ 44%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp +[ 45%] Linking CXX static library libnclextra.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +/usr/bin/ranlib libnclextra.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 45%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pda /build/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: + from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8354,16 +8234,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp -[ 59%] Linking CXX static library libyaml-cpp.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -[ 60%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp +[ 45%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8377,14 +8251,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" -/usr/bin/ranlib libyaml-cpp.a +[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp +[ 46%] Linking CXX static library libwhtest.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +[ 46%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp +cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +/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-2.0.7+dfsg/build.mpi' -[ 60%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8392,21 +8273,18 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 60%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp +[ 47%] Built target whtest +[ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8421,8 +8299,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: + from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8431,47 +8308,80 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 60%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 47%] Linking CXX static library libterraphast.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +/usr/bin/ranlib libterraphast.a In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, - from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 47%] Built target terraphast +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp +[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, + from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: + from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8481,20 +8391,97 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +[ 51%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp +[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp +[ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/map:60, + from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 54%] Linking CXX static library libncl.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o 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-2.0.7+dfsg/build.mpi' +[ 54%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/alignment /build/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +[ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8503,48 +8490,73 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/12/sstream:38, + from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, + from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp -[ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp +[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +[ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/split.h:25: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread 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-I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8560,38 +8572,61 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp +[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, - from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: + from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: + from /build/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp +[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/pda/ecopd.h:11, - from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8599,12 +8634,21 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp +[ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp +[ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, @@ -8619,84 +8663,84 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, + from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/pda/ecopd.h:11, + from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Linking CXX static library libncl.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o 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 +[ 66%] Linking CXX static library libutils.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' -[ 66%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +[ 66%] Built target utils +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/alignment /build/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/model /build/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +[ 66%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8704,13 +8748,12 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, @@ -8727,41 +8770,52 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp +[ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -8786,6 +8840,18 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8804,73 +8870,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 69%] Linking CXX static library libutils.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+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 +[ 68%] Linking CXX static library libyaml-cpp.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" +/usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 69%] Built target utils -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend +[ 68%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/model /build/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -[ 73%] Linking CXX static library libphyloYAML.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 -/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 73%] Built target phyloYAML +[ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8887,51 +8905,64 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, - from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8948,13 +8979,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { + | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8968,8 +9011,8 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: + from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8996,59 +9039,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, - from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/string:48, + from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 74%] Linking CXX static library libpda.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 74%] Built target pda -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/main /build/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build -make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 75%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9058,7 +9067,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9071,21 +9080,13 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: -/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ +/build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { + | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9104,6 +9105,7 @@ /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9116,24 +9118,22 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { - | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: +/build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 72%] Linking CXX static library libpda.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -9147,10 +9147,7 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp +/usr/bin/ranlib libpda.a /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9163,6 +9160,40 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 72%] Built target pda +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/main /build/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, + from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 73%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp +/build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); @@ -9176,6 +9207,9 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp +[ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9194,7 +9228,7 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: + from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9204,7 +9238,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, @@ -9226,6 +9260,20 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -9237,18 +9285,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +[ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp +[ 76%] Linking CXX static library libphyloYAML.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 +/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o +/usr/bin/ranlib libphyloYAML.a +make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' +[ 76%] Built target phyloYAML [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp -[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp -[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9263,6 +9312,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9277,6 +9328,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9291,8 +9344,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9323,18 +9376,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { - | ^~~~~ +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, @@ -9351,6 +9394,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, @@ -9369,20 +9426,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9419,6 +9462,10 @@ | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9431,8 +9478,6 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9466,10 +9511,6 @@ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -9486,6 +9527,27 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9510,33 +9572,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp [ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9549,22 +9586,24 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp +/build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -9572,15 +9611,17 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -9603,13 +9644,22 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: + from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /usr/include/c++/12/complex:45, + from /usr/include/eigen3/Eigen/Core:50, + from /usr/include/eigen3/Eigen/Dense:1, + from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -9617,7 +9667,7 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: + from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9627,44 +9677,23 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp +[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /usr/include/c++/12/complex:45, - from /usr/include/eigen3/Eigen/Core:50, - from /usr/include/eigen3/Eigen/Dense:1, - from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, - from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: + from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9677,9 +9706,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9692,7 +9720,22 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: +/build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, + from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9781,6 +9824,13 @@ /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 84%] Built target kernelsse +[ 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-2.0.7+dfsg/build.mpi' +[ 84%] Built target kernelavx [ 85%] 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 @@ -9788,27 +9838,20 @@ /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 85%] Built target kernelfma -[ 85%] 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 +[ 85%] Linking CXX static library libalignment.a +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake +cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 +/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +/usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' -[ 85%] Built target kernelavx +[ 85%] Built target alignment [ 86%] Linking CXX static library libmain.a cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o -[ 86%] Linking CXX static library libalignment.a -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake -cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 -/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libmain.a -/usr/bin/ranlib libalignment.a -make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 86%] Built target main -[ 86%] Built target alignment [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -9823,42 +9866,40 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, + from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9870,9 +9911,7 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9884,8 +9923,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9897,23 +9936,23 @@ | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9943,8 +9982,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, - from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9957,22 +9996,22 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9985,8 +10024,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10002,7 +10041,8 @@ from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10015,8 +10055,8 @@ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10031,7 +10071,8 @@ from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10045,19 +10086,22 @@ from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10067,39 +10111,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, - from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: -/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp -In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: @@ -10115,57 +10130,43 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/set:60, - from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/set:60, + from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] - 653 | } - | ^ -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] - 1298 | } - | ^ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: + from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10175,13 +10176,15 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: + from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10191,6 +10194,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -10205,6 +10210,22 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, @@ -10219,8 +10240,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o -cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp +In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: +/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -10249,6 +10282,8 @@ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -10265,6 +10300,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] + 653 | } + | ^ +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] + 1298 | } + | ^ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -10359,18 +10402,18 @@ echo 'time /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ... -+ time /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy ++ /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos15-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -Seed: 540558 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Sun May 26 20:48:54 2024 -Kernel: AVX - 1 threads (16 CPU cores detected) +Seed: 768452 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue Apr 25 17:00:57 2023 +Kernel: AVX - 1 threads (15 CPU cores detected) -HINT: Use -nt option to specify number of threads because your CPU has 16 cores! +HINT: Use -nt option to specify number of threads because your CPU has 15 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected @@ -10425,148 +10468,144 @@ **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) -Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.005 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) -1. Initial log-likelihood: -11278.874 -Optimal log-likelihood: -11278.756 -Rate parameters: A-C: 1.52235 A-G: 2.37813 A-T: 1.75542 C-G: 1.90960 C-T: 2.99649 G-T: 1.00000 +1. Initial log-likelihood: -11226.831 +Optimal log-likelihood: -11226.655 +Rate parameters: A-C: 1.43107 A-G: 2.31738 A-T: 1.73683 C-G: 1.90653 C-T: 2.79438 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 -Proportion of invariable sites: 0.084 -Gamma shape alpha: 1.409 -Parameters optimization took 1 rounds (0.194 sec) -Time for fast ML tree search: 2.472 seconds +Proportion of invariable sites: 0.085 +Gamma shape alpha: 1.515 +Parameters optimization took 1 rounds (0.073 sec) +Time for fast ML tree search: 0.687 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC - 1 GTR+F 11872.018 93 23930.037 23990.326 24297.446 - 2 GTR+F+I 11620.575 94 23429.149 23490.949 23800.510 - 3 GTR+F+G4 11292.573 94 22773.146 22834.945 23144.506 - 4 GTR+F+I+G4 11278.761 95 22747.521 22810.855 23122.832 - 5 GTR+F+R2 11401.184 95 22992.368 23055.701 23367.679 - 6 GTR+F+R3 11281.109 97 22756.217 22822.693 23139.430 - 7 GTR+F+R4 11272.436 99 22742.872 22812.590 23133.986 - 8 GTR+F+R5 11272.103 101 22746.206 22819.270 23145.221 - 17 SYM+I+G4 11284.886 92 22753.772 22812.577 23117.232 - 30 TVM+F+I+G4 11282.889 94 22753.778 22815.577 23125.138 - 43 TVMe+I+G4 11288.282 91 22758.564 22815.907 23118.073 - 56 TIM3+F+I+G4 11291.857 93 22769.714 22830.004 23137.124 - 69 TIM3e+I+G4 11298.317 90 22776.635 22832.539 23132.193 - 82 TIM2+F+I+G4 11295.475 93 22776.950 22837.240 23144.360 - 95 TIM2e+I+G4 11306.047 90 22792.094 22847.999 23147.652 -108 TIM+F+I+G4 11285.258 93 22756.516 22816.806 23123.926 -121 TIMe+I+G4 11295.055 90 22770.110 22826.015 23125.668 -134 TPM3u+F+I+G4 11296.211 92 22776.422 22835.226 23139.881 -147 TPM3+F+I+G4 11296.211 92 22776.422 22835.226 23139.881 -160 TPM2u+F+I+G4 11299.660 92 22783.320 22842.124 23146.779 -173 TPM2+F+I+G4 11299.660 92 22783.320 22842.124 23146.779 -186 K3Pu+F+I+G4 11289.410 92 22762.821 22821.625 23126.280 -199 K3P+I+G4 11298.327 89 22774.654 22829.144 23126.261 -212 TN+F+I+G4 11296.048 92 22776.096 22834.900 23139.555 -225 TNe+I+G4 11306.431 89 22790.861 22845.351 23142.468 -238 HKY+F+I+G4 11300.314 91 22782.628 22839.971 23142.137 -251 K2P+I+G4 11309.812 88 22795.624 22848.722 23143.281 -264 F81+F+I+G4 11353.444 90 22886.889 22942.793 23242.447 -277 JC+I+G4 11360.402 87 22894.804 22946.534 23238.510 + 1 GTR+F 11793.013 93 23772.026 23832.315 24139.435 + 2 GTR+F+I 11550.829 94 23289.659 23351.458 23661.019 + 3 GTR+F+G4 11242.079 94 22672.159 22733.958 23043.519 + 4 GTR+F+I+G4 11226.661 95 22643.323 22706.656 23018.634 + 5 GTR+F+R2 11338.371 95 22866.742 22930.076 23242.053 + 6 GTR+F+R3 11227.731 97 22649.462 22715.938 23032.675 + 7 GTR+F+R4 11220.639 99 22639.278 22708.997 23030.392 + 8 GTR+F+R5 11220.471 101 22642.943 22716.007 23041.958 + 17 SYM+I+G4 11229.747 92 22643.495 22702.299 23006.954 + 30 TVM+F+I+G4 11229.297 94 22646.593 22708.393 23017.954 + 43 TVMe+I+G4 11231.723 91 22645.446 22702.788 23004.954 + 56 TIM3+F+I+G4 11240.126 93 22666.252 22726.541 23033.661 + 69 TIM3e+I+G4 11243.927 90 22667.855 22723.759 23023.412 + 82 TIM2+F+I+G4 11243.512 93 22673.024 22733.314 23040.434 + 95 TIM2e+I+G4 11251.105 90 22682.209 22738.114 23037.767 +108 TIM+F+I+G4 11231.522 93 22649.043 22709.333 23016.453 +121 TIMe+I+G4 11238.215 90 22656.431 22712.335 23011.989 +134 TPM3u+F+I+G4 11242.898 92 22669.795 22728.599 23033.254 +147 TPM3+F+I+G4 11242.898 92 22669.795 22728.599 23033.254 +160 TPM2u+F+I+G4 11246.207 92 22676.414 22735.218 23039.873 +173 TPM2+F+I+G4 11246.207 92 22676.414 22735.218 23039.873 +186 K3Pu+F+I+G4 11234.112 92 22652.223 22711.027 23015.682 +199 K3P+I+G4 11240.039 89 22658.077 22712.567 23009.684 +212 TN+F+I+G4 11243.591 92 22671.182 22729.986 23034.641 +225 TNe+I+G4 11251.122 89 22680.243 22734.733 23031.850 +238 HKY+F+I+G4 11246.299 91 22674.598 22731.941 23034.107 +251 K2P+I+G4 11253.033 88 22682.065 22735.163 23029.722 +264 F81+F+I+G4 11295.168 90 22770.336 22826.241 23125.894 +277 JC+I+G4 11299.159 87 22772.319 22824.048 23116.025 Akaike Information Criterion: GTR+F+R4 -Corrected Akaike Information Criterion: GTR+F+I+G4 -Bayesian Information Criterion: SYM+I+G4 -Best-fit model: SYM+I+G4 chosen according to BIC +Corrected Akaike Information Criterion: SYM+I+G4 +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: 9.092 seconds (0h:0m:9s) -Wall-clock time for ModelFinder: 30.177 seconds (0h:0m:30s) +CPU time for ModelFinder: 5.538 seconds (0h:0m:5s) +Wall-clock time for ModelFinder: 5.562 seconds (0h:0m:5s) 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, 1.445 / Estimate: 0.000, 0.890 / LogL: -11298.276 -Init pinv, alpha: 0.012, 1.445 / Estimate: 0.083, 1.432 / LogL: -11284.881 -Init pinv, alpha: 0.023, 1.445 / Estimate: 0.083, 1.430 / LogL: -11284.879 -Init pinv, alpha: 0.035, 1.445 / Estimate: 0.083, 1.431 / LogL: -11284.885 -Init pinv, alpha: 0.046, 1.445 / Estimate: 0.083, 1.435 / LogL: -11284.879 -Init pinv, alpha: 0.058, 1.445 / Estimate: 0.083, 1.432 / LogL: -11284.877 -Init pinv, alpha: 0.069, 1.445 / Estimate: 0.083, 1.429 / LogL: -11284.887 -Init pinv, alpha: 0.081, 1.445 / Estimate: 0.083, 1.435 / LogL: -11284.873 -Init pinv, alpha: 0.093, 1.445 / Estimate: 0.085, 1.449 / LogL: -11284.882 -Init pinv, alpha: 0.104, 1.445 / Estimate: 0.085, 1.455 / LogL: -11284.890 -Optimal pinv,alpha: 0.083, 1.435 / LogL: -11284.873 +Init pinv, alpha: 0.000, 1.555 / Estimate: 0.000, 0.956 / LogL: -11246.171 +Init pinv, alpha: 0.012, 1.555 / Estimate: 0.083, 1.547 / LogL: -11231.718 +Init pinv, alpha: 0.023, 1.555 / Estimate: 0.083, 1.544 / LogL: -11231.720 +Init pinv, alpha: 0.035, 1.555 / Estimate: 0.083, 1.542 / LogL: -11231.722 +Init pinv, alpha: 0.046, 1.555 / Estimate: 0.083, 1.546 / LogL: -11231.720 +Init pinv, alpha: 0.058, 1.555 / Estimate: 0.083, 1.543 / LogL: -11231.725 +Init pinv, alpha: 0.069, 1.555 / Estimate: 0.083, 1.540 / LogL: -11231.728 +Init pinv, alpha: 0.081, 1.555 / Estimate: 0.083, 1.546 / LogL: -11231.723 +Init pinv, alpha: 0.093, 1.555 / Estimate: 0.085, 1.558 / LogL: -11231.721 +Init pinv, alpha: 0.104, 1.555 / Estimate: 0.085, 1.564 / LogL: -11231.729 +Optimal pinv,alpha: 0.083, 1.547 / LogL: -11231.718 -Parameters optimization took 9.160 sec -Computing ML distances based on estimated model parameters... 0.059 sec +Parameters optimization took 1.972 sec +Computing ML distances based on estimated model parameters... 0.052 sec Computing BIONJ tree... 0.002 seconds -Log-likelihood of BIONJ tree: -11269.983 +Log-likelihood of BIONJ tree: -11270.883 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 1.982 second -Computing log-likelihood of 98 initial trees ... 5.810 seconds -Current best score: -11253.469 +Generating 98 parsimony trees... 0.811 second +Computing log-likelihood of 98 initial trees ... 1.375 seconds +Current best score: -11231.718 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11222.937 -Iteration 10 / LogL: -11229.927 / Time: 0h:0m:29s -Iteration 20 / LogL: -11230.124 / Time: 0h:0m:42s -Finish initializing candidate tree set (13) -Current best tree score: -11222.937 / CPU time: 33.336 +BETTER TREE FOUND at iteration 1: -11231.655 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 2: -11225.144 +Iteration 10 / LogL: -11231.227 / Time: 0h:0m:7s +Iteration 20 / LogL: -11244.731 / Time: 0h:0m:9s +Finish initializing candidate tree set (17) +Current best tree score: -11225.144 / CPU time: 7.834 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- +Iteration 30 / LogL: -11225.625 / Time: 0h:0m:12s (0h:0m:31s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 24: -11222.757 -Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 30: -11222.594 -Iteration 30 / LogL: -11222.594 / Time: 0h:1m:3s (0h:3m:37s left) -Iteration 40 / LogL: -11222.761 / Time: 0h:1m:21s (0h:3m:7s left) -Iteration 50 / LogL: -11224.270 / Time: 0h:1m:38s (0h:2m:40s left) -Iteration 60 / LogL: -11235.178 / Time: 0h:1m:55s (0h:2m:16s left) -Iteration 70 / LogL: -11222.629 / Time: 0h:2m:8s (0h:1m:51s left) -Iteration 80 / LogL: -11224.197 / Time: 0h:2m:18s (0h:1m:27s left) -Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 89: -11222.113 -Iteration 90 / LogL: -11224.793 / Time: 0h:2m:37s (0h:2m:55s left) +BETTER TREE FOUND at iteration 38: -11224.096 +Iteration 40 / LogL: -11224.145 / Time: 0h:0m:15s (0h:0m:39s left) +BETTER TREE FOUND at iteration 41: -11224.086 +Iteration 50 / LogL: -11225.452 / Time: 0h:0m:19s (0h:0m:36s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 96: -11221.031 -Iteration 100 / LogL: -11222.270 / Time: 0h:2m:54s (0h:2m:49s left) -Iteration 110 / LogL: -11222.150 / Time: 0h:3m:11s (0h:2m:31s left) -Iteration 120 / LogL: -11228.334 / Time: 0h:3m:24s (0h:2m:10s left) +BETTER TREE FOUND at iteration 52: -11222.902 +Iteration 60 / LogL: -11224.433 / Time: 0h:0m:22s (0h:0m:35s left) Estimate model parameters (epsilon = 0.100) -UPDATE BEST LOG-LIKELIHOOD: -11220.898 -Iteration 130 / LogL: -11220.904 / Time: 0h:3m:33s (0h:1m:49s left) -Iteration 140 / LogL: -11222.276 / Time: 0h:3m:40s (0h:1m:28s left) -Iteration 150 / LogL: -11235.135 / Time: 0h:3m:46s (0h:1m:9s left) -Iteration 160 / LogL: -11220.937 / Time: 0h:3m:52s (0h:0m:52s left) -Iteration 170 / LogL: -11233.341 / Time: 0h:3m:57s (0h:0m:36s left) -Iteration 180 / LogL: -11221.695 / Time: 0h:4m:2s (0h:0m:21s left) -Iteration 190 / LogL: -11221.276 / Time: 0h:4m:9s (0h:0m:7s left) -TREE SEARCH COMPLETED AFTER 197 ITERATIONS / Time: 0h:4m:14s +BETTER TREE FOUND at iteration 61: -11222.780 +Iteration 70 / LogL: -11224.462 / Time: 0h:0m:25s (0h:0m:33s left) +Iteration 80 / LogL: -11224.146 / Time: 0h:0m:27s (0h:0m:28s left) +Iteration 90 / LogL: -11222.962 / Time: 0h:0m:30s (0h:0m:23s left) +Iteration 100 / LogL: -11241.216 / Time: 0h:0m:32s (0h:0m:19s left) +Iteration 110 / LogL: -11222.800 / Time: 0h:0m:34s (0h:0m:16s left) +Iteration 120 / LogL: -11223.099 / Time: 0h:0m:37s (0h:0m:12s left) +Iteration 130 / LogL: -11222.831 / Time: 0h:0m:40s (0h:0m:9s left) +Iteration 140 / LogL: -11231.750 / Time: 0h:0m:42s (0h:0m:6s left) +Iteration 150 / LogL: -11222.790 / Time: 0h:0m:45s (0h:0m:3s left) +Iteration 160 / LogL: -11227.300 / Time: 0h:0m:47s (0h:0m:0s left) +TREE SEARCH COMPLETED AFTER 162 ITERATIONS / Time: 0h:0m:48s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11220.898 -Optimal log-likelihood: -11220.892 -Rate parameters: A-C: 1.52930 A-G: 2.42612 A-T: 1.66909 C-G: 2.00225 C-T: 2.84350 G-T: 1.00000 +1. Initial log-likelihood: -11222.780 +Optimal log-likelihood: -11222.778 +Rate parameters: A-C: 1.53470 A-G: 2.63887 A-T: 1.69662 C-G: 2.00946 C-T: 2.63887 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: 1.533 -Parameters optimization took 1 rounds (0.109 sec) -BEST SCORE FOUND : -11220.892 -Total tree length: 12.595 - -Total number of iterations: 197 -CPU time used for tree search: 102.676 sec (0h:1m:42s) -Wall-clock time used for tree search: 245.151 sec (0h:4m:5s) -Total CPU time used: 106.408 sec (0h:1m:46s) -Total wall-clock time used: 254.800 sec (0h:4m:14s) +Gamma shape alpha: 1.530 +Parameters optimization took 1 rounds (0.046 sec) +BEST SCORE FOUND : -11222.778 +Total tree length: 12.601 + +Total number of iterations: 162 +CPU time used for tree search: 45.247 sec (0h:0m:45s) +Wall-clock time used for tree search: 46.369 sec (0h:0m:46s) +Total CPU time used: 47.389 sec (0h:0m:47s) +Total wall-clock time used: 48.520 sec (0h:0m:48s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -10574,21 +10613,23 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Sun May 26 20:53:39 2024 -115.51user 1.52system 4:45.05elapsed 41%CPU (0avgtext+0avgdata 14216maxresident)k -64inputs+0outputs (4major+2016minor)pagefaults 0swaps -+ time /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo +Date and Time: Tue Apr 25 17:01:51 2023 + +real 0m54.094s +user 0m52.928s +sys 0m0.683s ++ /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos15-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo -Seed: 584878 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Sun May 26 20:53:39 2024 -Kernel: AVX - 1 threads (16 CPU cores detected) +Seed: 862906 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue Apr 25 17:01:51 2023 +Kernel: AVX - 1 threads (15 CPU cores detected) -HINT: Use -nt option to specify number of threads because your CPU has 16 cores! +HINT: Use -nt option to specify number of threads because your CPU has 15 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected @@ -10643,139 +10684,145 @@ **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) -Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.008 seconds +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) -1. Initial log-likelihood: -11222.583 -Optimal log-likelihood: -11222.469 -Rate parameters: A-C: 1.46888 A-G: 2.34107 A-T: 1.77635 C-G: 1.90931 C-T: 2.84690 G-T: 1.00000 +1. Initial log-likelihood: -11239.760 +Optimal log-likelihood: -11239.649 +Rate parameters: A-C: 1.45046 A-G: 2.32044 A-T: 1.74141 C-G: 1.90741 C-T: 2.78602 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 -Gamma shape alpha: 1.531 -Parameters optimization took 1 rounds (0.087 sec) -Time for fast ML tree search: 1.028 seconds +Gamma shape alpha: 1.549 +Parameters optimization took 1 rounds (0.048 sec) +Time for fast ML tree search: 0.528 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC - 1 GTR+F 11784.865 93 23755.731 23816.021 24123.141 - 2 GTR+F+I 11542.762 94 23273.525 23335.324 23644.885 - 3 GTR+F+G4 11238.124 94 22664.249 22726.048 23035.609 - 4 GTR+F+I+G4 11222.470 95 22634.941 22698.274 23010.252 - 5 GTR+F+R2 11332.079 95 22854.159 22917.492 23229.470 - 6 GTR+F+R3 11222.904 97 22639.808 22706.283 23023.020 - 7 GTR+F+R4 11216.558 99 22631.117 22700.835 23022.231 - 8 GTR+F+R5 11216.196 101 22634.392 22707.456 23033.407 - 17 SYM+I+G4 11225.577 92 22635.154 22693.958 22998.613 - 30 TVM+F+I+G4 11225.427 94 22638.855 22700.654 23010.215 - 43 TVMe+I+G4 11227.870 91 22637.741 22695.083 22997.249 - 56 TIM3+F+I+G4 11237.296 93 22660.592 22720.881 23028.001 - 69 TIM3e+I+G4 11240.994 90 22661.988 22717.892 23017.545 - 82 TIM2+F+I+G4 11240.874 93 22667.748 22728.038 23035.158 - 95 TIM2e+I+G4 11248.653 90 22677.305 22733.210 23032.863 -108 TIM+F+I+G4 11228.664 93 22643.327 22703.617 23010.737 -121 TIMe+I+G4 11235.522 90 22651.043 22706.948 23006.601 -134 TPM3u+F+I+G4 11240.439 92 22664.878 22723.682 23028.337 -147 TPM3+F+I+G4 11240.439 92 22664.878 22723.682 23028.337 -160 TPM2u+F+I+G4 11243.911 92 22671.821 22730.625 23035.280 -173 TPM2+F+I+G4 11243.911 92 22671.821 22730.625 23035.280 -186 K3Pu+F+I+G4 11231.608 92 22647.215 22706.019 23010.674 -199 K3P+I+G4 11237.658 89 22653.317 22707.806 23004.924 -212 TN+F+I+G4 11241.228 92 22666.457 22725.261 23029.916 -225 TNe+I+G4 11248.858 89 22675.716 22730.205 23027.323 -238 HKY+F+I+G4 11244.294 91 22670.587 22727.930 23030.096 -251 K2P+I+G4 11251.083 88 22678.166 22731.264 23025.823 -264 F81+F+I+G4 11294.363 90 22768.726 22824.630 23124.283 -277 JC+I+G4 11298.377 87 22770.754 22822.484 23114.460 + 1 GTR+F 11797.808 93 23781.615 23841.905 24149.025 + 2 GTR+F+I 11556.535 94 23301.070 23362.869 23672.430 + 3 GTR+F+G4 11255.917 94 22699.833 22761.633 23071.194 + 4 GTR+F+I+G4 11239.658 95 22669.316 22732.649 23044.627 + 5 GTR+F+R2 11346.095 95 22882.189 22945.522 23257.500 + 6 GTR+F+R3 11241.184 97 22676.368 22742.843 23059.580 + 7 GTR+F+R4 11233.752 99 22665.504 22735.223 23056.618 + 8 GTR+F+R5 11233.332 101 22668.665 22741.728 23067.680 + 17 SYM+I+G4 11242.729 92 22669.457 22728.261 23032.916 + 30 TVM+F+I+G4 11242.143 94 22672.286 22734.085 23043.646 + 43 TVMe+I+G4 11244.615 91 22671.230 22728.573 23030.739 + 56 TIM3+F+I+G4 11253.755 93 22693.511 22753.800 23060.920 + 69 TIM3e+I+G4 11257.581 90 22695.161 22751.066 23050.719 + 82 TIM2+F+I+G4 11257.451 93 22700.903 22761.192 23068.312 + 95 TIM2e+I+G4 11265.345 90 22710.689 22766.594 23066.247 +108 TIM+F+I+G4 11245.392 93 22676.783 22737.073 23044.193 +121 TIMe+I+G4 11252.268 90 22684.536 22740.441 23040.094 +134 TPM3u+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 +147 TPM3+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 +160 TPM2u+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 +173 TPM2+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 +186 K3Pu+F+I+G4 11247.847 92 22679.694 22738.498 23043.153 +199 K3P+I+G4 11254.005 89 22686.010 22740.500 23037.617 +212 TN+F+I+G4 11257.649 92 22699.298 22758.102 23062.757 +225 TNe+I+G4 11265.431 89 22708.861 22763.351 23060.468 +238 HKY+F+I+G4 11260.239 91 22702.477 22759.820 23061.986 +251 K2P+I+G4 11267.270 88 22710.539 22763.638 23058.196 +264 F81+F+I+G4 11308.833 90 22797.666 22853.571 23153.224 +277 JC+I+G4 11313.164 87 22800.329 22852.059 23144.035 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 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: 7.627 seconds (0h:0m:7s) -Wall-clock time for ModelFinder: 8.468 seconds (0h:0m:8s) +CPU time for ModelFinder: 5.411 seconds (0h:0m:5s) +Wall-clock time for ModelFinder: 5.480 seconds (0h:0m:5s) 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, 1.576 / Estimate: 0.000, 0.961 / LogL: -11242.445 -Init pinv, alpha: 0.012, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.870 -Init pinv, alpha: 0.023, 1.576 / Estimate: 0.084, 1.565 / LogL: -11227.872 -Init pinv, alpha: 0.035, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.874 -Init pinv, alpha: 0.046, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.872 -Init pinv, alpha: 0.058, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.875 -Init pinv, alpha: 0.069, 1.576 / Estimate: 0.083, 1.562 / LogL: -11227.877 -Init pinv, alpha: 0.081, 1.576 / Estimate: 0.084, 1.566 / LogL: -11227.871 -Init pinv, alpha: 0.093, 1.576 / Estimate: 0.085, 1.579 / LogL: -11227.871 -Init pinv, alpha: 0.104, 1.576 / Estimate: 0.085, 1.585 / LogL: -11227.877 -Optimal pinv,alpha: 0.084, 1.568 / LogL: -11227.870 +Init pinv, alpha: 0.000, 1.590 / Estimate: 0.000, 0.970 / LogL: -11259.840 +Init pinv, alpha: 0.012, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.628 +Init pinv, alpha: 0.023, 1.590 / Estimate: 0.084, 1.581 / LogL: -11244.611 +Init pinv, alpha: 0.035, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.613 +Init pinv, alpha: 0.046, 1.590 / Estimate: 0.084, 1.582 / LogL: -11244.612 +Init pinv, alpha: 0.058, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.618 +Init pinv, alpha: 0.069, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.620 +Init pinv, alpha: 0.081, 1.590 / Estimate: 0.084, 1.580 / LogL: -11244.615 +Init pinv, alpha: 0.093, 1.590 / Estimate: 0.085, 1.592 / LogL: -11244.613 +Init pinv, alpha: 0.104, 1.590 / Estimate: 0.086, 1.598 / LogL: -11244.621 +Optimal pinv,alpha: 0.084, 1.581 / LogL: -11244.611 -Parameters optimization took 3.642 sec -Computing ML distances based on estimated model parameters... 0.058 sec +Parameters optimization took 1.812 sec +Computing ML distances based on estimated model parameters... 0.046 sec Computing BIONJ tree... -0.006 seconds -Log-likelihood of BIONJ tree: -11270.856 +0.002 seconds +Log-likelihood of BIONJ tree: -11270.724 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 0.944 second -Computing log-likelihood of 98 initial trees ... 3.010 seconds -Current best score: -11227.870 +Generating 98 parsimony trees... 0.706 second +Computing log-likelihood of 98 initial trees ... 1.267 seconds +Current best score: -11244.611 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11226.734 +BETTER TREE FOUND at iteration 1: -11244.583 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 2: -11225.137 -Iteration 10 / LogL: -11226.927 / Time: 0h:0m:12s -Iteration 20 / LogL: -11226.926 / Time: 0h:0m:18s -Finish initializing candidate tree set (13) -Current best tree score: -11225.137 / CPU time: 14.283 +BETTER TREE FOUND at iteration 2: -11225.129 +Iteration 10 / LogL: -11232.240 / Time: 0h:0m:5s +Iteration 20 / LogL: -11231.938 / Time: 0h:0m:8s +Finish initializing candidate tree set (14) +Current best tree score: -11225.129 / CPU time: 6.229 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -11235.709 / Time: 0h:0m:27s (0h:1m:7s left) +Iteration 30 / LogL: -11225.347 / Time: 0h:0m:11s (0h:0m:27s left) +Iteration 40 / LogL: -11237.948 / Time: 0h:0m:13s (0h:0m:21s left) +UPDATE BEST LOG-LIKELIHOOD: -11225.129 +Iteration 50 / LogL: -11225.279 / Time: 0h:0m:16s (0h:0m:17s left) +Iteration 60 / LogL: -11231.806 / Time: 0h:0m:19s (0h:0m:13s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 33: -11222.904 -Iteration 40 / LogL: -11225.506 / Time: 0h:0m:41s (0h:1m:39s left) +BETTER TREE FOUND at iteration 64: -11222.898 +Iteration 70 / LogL: -11225.249 / Time: 0h:0m:22s (0h:0m:30s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 44: -11222.785 -Iteration 50 / LogL: -11223.077 / Time: 0h:0m:58s (0h:1m:53s left) -Iteration 60 / LogL: -11223.003 / Time: 0h:1m:13s (0h:1m:44s left) -Iteration 70 / LogL: -11222.870 / Time: 0h:1m:23s (0h:1m:29s left) -Iteration 80 / LogL: -11222.829 / Time: 0h:1m:35s (0h:1m:17s left) -Iteration 90 / LogL: -11228.753 / Time: 0h:1m:49s (0h:1m:6s left) -Iteration 100 / LogL: -11222.943 / Time: 0h:2m:3s (0h:0m:54s left) -Iteration 110 / LogL: -11226.133 / Time: 0h:2m:13s (0h:0m:41s left) -Iteration 120 / LogL: -11222.800 / Time: 0h:2m:34s (0h:0m:31s left) -Iteration 130 / LogL: -11223.251 / Time: 0h:2m:48s (0h:0m:18s left) -Iteration 140 / LogL: -11223.621 / Time: 0h:3m:3s (0h:0m:5s left) -TREE SEARCH COMPLETED AFTER 145 ITERATIONS / Time: 0h:3m:9s +BETTER TREE FOUND at iteration 80: -11222.776 +Iteration 80 / LogL: -11222.776 / Time: 0h:0m:25s (0h:0m:32s left) +Iteration 90 / LogL: -11224.114 / Time: 0h:0m:30s (0h:0m:30s left) +Iteration 100 / LogL: -11222.925 / Time: 0h:0m:33s (0h:0m:26s left) +Iteration 110 / LogL: -11226.476 / Time: 0h:0m:35s (0h:0m:22s left) +Iteration 120 / LogL: -11222.927 / Time: 0h:0m:38s (0h:0m:19s left) +Iteration 130 / LogL: -11222.795 / Time: 0h:0m:40s (0h:0m:15s left) +Iteration 140 / LogL: -11223.317 / Time: 0h:0m:44s (0h:0m:12s left) +Iteration 150 / LogL: -11223.131 / Time: 0h:0m:47s (0h:0m:9s left) +Iteration 160 / LogL: -11223.097 / Time: 0h:0m:49s (0h:0m:6s left) +UPDATE BEST LOG-LIKELIHOOD: -11222.775 +Iteration 170 / LogL: -11223.153 / Time: 0h:0m:52s (0h:0m:3s left) +Iteration 180 / LogL: -11226.283 / Time: 0h:0m:55s (0h:0m:0s left) +TREE SEARCH COMPLETED AFTER 181 ITERATIONS / Time: 0h:0m:55s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11222.785 -Optimal log-likelihood: -11222.781 -Rate parameters: A-C: 1.54136 A-G: 2.64404 A-T: 1.70145 C-G: 2.01309 C-T: 2.64404 G-T: 1.00000 +1. Initial log-likelihood: -11222.775 +Optimal log-likelihood: -11222.772 +Rate parameters: A-C: 1.51825 A-G: 2.61371 A-T: 1.67570 C-G: 1.98422 C-T: 2.61371 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 -Proportion of invariable sites: 0.083 -Gamma shape alpha: 1.529 -Parameters optimization took 1 rounds (0.126 sec) -BEST SCORE FOUND : -11222.781 -Total tree length: 12.598 - -Total number of iterations: 145 -CPU time used for tree search: 78.514 sec (0h:1m:18s) -Wall-clock time used for tree search: 185.395 sec (0h:3m:5s) -Total CPU time used: 81.814 sec (0h:1m:21s) -Total wall-clock time used: 189.394 sec (0h:3m:9s) +Proportion of invariable sites: 0.084 +Gamma shape alpha: 1.530 +Parameters optimization took 1 rounds (0.045 sec) +BEST SCORE FOUND : -11222.772 +Total tree length: 12.605 + +Total number of iterations: 181 +CPU time used for tree search: 50.942 sec (0h:0m:50s) +Wall-clock time used for tree search: 53.823 sec (0h:0m:53s) +Total CPU time used: 52.923 sec (0h:0m:52s) +Total wall-clock time used: 55.804 sec (0h:0m:55s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -10783,12 +10830,14 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Sun May 26 20:56:57 2024 -89.44user 0.95system 3:17.88elapsed 45%CPU (0avgtext+0avgdata 14676maxresident)k -0inputs+0outputs (0major+3579minor)pagefaults 0swaps -+ rm -rf /tmp/iqtree-test.oKRBCq -204.98user 2.54system 8:03.91elapsed 42%CPU (0avgtext+0avgdata 14676maxresident)k -1152inputs+0outputs (54major+7075minor)pagefaults 0swaps +Date and Time: Tue Apr 25 17:02:53 2023 + +real 1m1.299s +user 0m58.337s +sys 0m0.644s ++ rm -rf /tmp/iqtree-test.wnqM2S +111.29user 1.35system 1:55.44elapsed 97%CPU (0avgtext+0avgdata 15732maxresident)k +0inputs+0outputs (0major+6631minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' create-stamp debian/debhelper-build-stamp @@ -10797,7 +10846,7 @@ make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi - cd build.serial && make -j16 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.serial && make -j15 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -10815,7 +10864,7 @@ -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi - cd build.mpi && make -j16 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.mpi && make -j15 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -10878,8 +10927,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1_amd64.deb'. +dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -10887,12 +10936,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/446769/tmp/hooks/B01_cleanup finished 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/2789017 and its subdirectories -I: Current time: Sun May 26 21:05:53 -12 2024 -I: pbuilder-time-stamp: 1716800753 +I: removing directory /srv/workspace/pbuilder/446769 and its subdirectories +I: Current time: Tue Apr 25 17:04:59 +14 2023 +I: pbuilder-time-stamp: 1682391899