Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 01:59:16.358522906 +0000 +++ b2/build.log 2023-06-06 02:35:40.950755665 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 5 12:58:24 -12 2023 -I: pbuilder-time-stamp: 1686013104 +I: Current time: Tue Jun 6 16:02:42 +14 2023 +I: pbuilder-time-stamp: 1686016962 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 [./libbpp-phyl_2.4.1.orig.tar.gz] I: copying [./libbpp-phyl_2.4.1-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 30 05:58:43 2022 -12 +gpgv: Signature made Thu Dec 1 07:58:43 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ dpkg-source: info: applying remove_test_likelihood_nh.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6221/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13264/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 Jun 6 16:02 /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/13264/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13264/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='4fe1b647aa7049568e6c7cd6f7c0f9ba' - 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='6221' - PS1='# ' - PS2='> ' + INVOCATION_ID=78af617142a64d79957aa66893191d1d + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=13264 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.3kGK0zjJ/pbuilderrc_eRyf --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.3kGK0zjJ/b1 --logfile b1/build.log libbpp-phyl_2.4.1-8.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.3kGK0zjJ/pbuilderrc_bk5h --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.3kGK0zjJ/b2 --logfile b2/build.log --extrapackages usrmerge libbpp-phyl_2.4.1-8.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/6221/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 6 16:02 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/13264/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 51 http://deb.debian.org/debian bookworm/main armhf libbpp-core-dev armhf 2.4.1-9 [943 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libbpp-seq12 armhf 2.4.1-9 [420 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libbpp-seq-dev armhf 2.4.1-9 [733 kB] -Fetched 29.6 MB in 1s (43.0 MB/s) +Fetched 29.6 MB in 1s (36.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19324 files and directories currently installed.) @@ -478,8 +510,19 @@ 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/libbpp-phyl-2.4.1/ && 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 > ../libbpp-phyl_2.4.1-8_source.changes +I: user script /srv/workspace/pbuilder/13264/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/13264/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libbpp-phyl-2.4.1/ && 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 > ../libbpp-phyl_2.4.1-8_source.changes dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-8 dpkg-buildpackage: info: source distribution unstable @@ -530,7 +573,7 @@ -- Build files have been written to: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-phyl-2.4.1 -B/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -539,21 +582,23 @@ make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/depend make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake --color= +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o [ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o [ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp -[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, @@ -570,6 +615,24 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp [ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp In file included from /usr/include/c++/12/vector:70, @@ -592,7 +655,9 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, @@ -622,11 +687,29 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp +[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -646,24 +729,28 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp +[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/../StateMap.h:44, @@ -681,9 +768,26 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -707,9 +811,31 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -728,26 +854,49 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp +[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, @@ -787,30 +936,47 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp +[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp +[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o +[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, @@ -845,11 +1011,35 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp +[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o +[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp +[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -869,30 +1059,35 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp +[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp +[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp +[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, @@ -906,16 +1101,38 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:763:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:763:30: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -928,30 +1145,51 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41: + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43, + from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43, + from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:119:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:124:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:146:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:147:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:172:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:119:23: @@ -981,65 +1219,46 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp +[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o +[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp +[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o +[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp +[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp +[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp +[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp +[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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+[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp +[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp +[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeTemplate.h:351:69: + inlined from 'static bpp::PairedSiteLikelihoods bpp::IOTreepuzzlePairedSiteLikelihoods::read(std::istream&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:106:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp -[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp -[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp -[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp In file included from /usr/include/c++/12/vector:70, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -1062,53 +1281,55 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp -[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp -[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'static std::vector bpp::IOPhymlPairedSiteLikelihoods::read(std::istream&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:261:29: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp +[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -MF 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/usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp +[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp +[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../TreeExceptions.h:44, @@ -1126,32 +1347,35 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o +[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp +[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp +[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o +[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp +[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1171,26 +1395,32 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o +[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp +[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp +[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1209,14 +1439,23 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp -[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o +[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp -[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp +[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 189 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1243,12 +1482,27 @@ /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o +In file included from /usr/include/c++/12/vector:64: +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:211:30, + inlined from 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:225:32: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:212:31, + inlined from 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:225:32: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp +[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o +[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp +[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1268,6 +1522,33 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -1284,6 +1565,20 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:137:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:137:22: @@ -1295,6 +1590,31 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:137:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:261:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:261:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:261:7: @@ -1315,24 +1635,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:763:30: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1346,12 +1648,14 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o +[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1361,6 +1665,52 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:180:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:180:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:180:7: @@ -1381,8 +1731,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1397,8 +1745,20 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1416,6 +1776,31 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -1424,8 +1809,10 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o +[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp +[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:184:7: @@ -1446,10 +1833,30 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp -[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:184:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:184:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp +[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1465,52 +1872,23 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43, - from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43, - from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40: + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 -[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:119:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:124:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:146:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:147:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const std::string&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:172:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Utils/MapTools.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, @@ -1540,6 +1918,49 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Utils/MapTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:85:50: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:91:59: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1554,8 +1975,10 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/SymbolList.h:43, @@ -1573,7 +1996,26 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /usr/include/Bpp/Seq/SymbolList.h:43, + from /usr/include/Bpp/Seq/Sequence.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../AncestralStateReconstruction.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp +[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, @@ -1594,6 +2036,33 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -1622,8 +2091,45 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'void bpp::BranchLikelihood::computeLogLikelihood()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:115:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'void bpp::BranchLikelihood::computeLogLikelihood()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:115:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Utils/MapTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::NNIHomogeneousTreeLikelihood::doNNI(int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:337:43: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Utils/MapTools.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46: @@ -1631,6 +2137,15 @@ /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual double bpp::NNIHomogeneousTreeLikelihood::testNNI(int) const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:303:25: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'virtual void bpp::NNIHomogeneousTreeLikelihood::doNNI(int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:337:43: @@ -1650,11 +2165,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o +[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp -[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp -[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp +[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Utils/MapTools.h:43, @@ -1689,7 +2212,96 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Utils/MapTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:147:52: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:153:59: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:129:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:129:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, const bpp::SiteContainer&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:99:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:73:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, const bpp::SiteContainer&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:99:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:73:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -1717,8 +2329,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -1735,6 +2345,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, const bpp::SiteContainer&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:99:22: @@ -1747,7 +2359,7 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o +[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, @@ -1775,6 +2387,52 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:170:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:170:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:170:7: @@ -1795,8 +2453,46 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:730:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:737:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1811,8 +2507,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1827,8 +2521,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:730:21: @@ -1841,12 +2533,14 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o +[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp +[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp +[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp +[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1864,6 +2558,8 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionMethods.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -1872,7 +2568,32 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionMethods.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, @@ -1894,30 +2615,40 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:176:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:176:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41: + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'static bpp::PairedSiteLikelihoods bpp::IOTreepuzzlePairedSiteLikelihoods::read(std::istream&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:106:38: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'static std::vector bpp::IOPhymlPairedSiteLikelihoods::read(std::istream&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:261:29: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1932,30 +2663,54 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp -[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o +[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp +[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp +[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o +[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o +[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp +[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o +[ 32%] Building CXX object 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o +[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp +[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp +[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o +[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, @@ -1974,27 +2729,28 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, @@ -2013,10 +2769,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o +[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, @@ -2036,36 +2790,40 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp +[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o +[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp +[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o +[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp +[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -2086,36 +2844,41 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp -[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp +[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp +[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp -[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o +[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -2159,38 +2922,57 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41: -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 189 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp In file included from /usr/include/c++/12/vector:64: -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:211:30, - inlined from 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:225:32: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:212:31, - inlined from 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:225:32: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:98:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:99:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:80:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:81:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:80:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:81:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -2284,6 +3066,20 @@ from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -2301,11 +3097,109 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45: +/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:414:34: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:422:76: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:422:46: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:428:34: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:442:36: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:446:76: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:446:46: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::AbstractSubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:144:31: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::AbstractSubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:145:32: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp +[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp -[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp -[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o +[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, @@ -2340,284 +3234,161 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o +[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp +[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp +[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::BinarySubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:238:19: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::BinarySubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:238:30: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:137:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:137:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:261:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:261:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp -[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o +[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp +[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp +[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -c 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-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o +[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp +[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp +[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp -[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o +[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:180:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:180:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o +[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp +[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp +[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o.d -o 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o +[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp +[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp +[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp -[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:184:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:184:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp -[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o +[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KCM.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/GY94.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o +[ 50%] Building CXX object 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp -[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o +[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -MF 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp -[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp -[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o +[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp -[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o +[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/MG94.cpp +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/MG94.cpp -[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Utils/MapTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43, + from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:85:50: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:115:22: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:91:59: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:116:27: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp -[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:120:22: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YN98.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -2660,30 +3431,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o +[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp +[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YN98.cpp -[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /usr/include/Bpp/Seq/SymbolList.h:43, - from /usr/include/Bpp/Seq/Sequence.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../AncestralStateReconstruction.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp -[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, @@ -2759,35 +3517,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, @@ -2808,26 +3539,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'void bpp::BranchLikelihood::computeLogLikelihood()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:115:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'void bpp::BranchLikelihood::computeLogLikelihood()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:115:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: @@ -2840,6 +3551,32 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M1::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:135:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M1::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:136:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: @@ -2852,36 +3589,104 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Utils/MapTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::NNIHomogeneousTreeLikelihood::doNNI(int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:337:43: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual double bpp::NNIHomogeneousTreeLikelihood::testNNI(int) const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:303:25: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M10::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:151:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp +[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, @@ -2986,10 +3791,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, @@ -3004,6 +3805,132 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M3::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:182:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:140:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:141:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:142:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:61:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:64:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:69:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:51: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:39: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:63: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:61:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:64:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:69:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void bpp::YNGP_M3::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:182:17: @@ -3030,6 +3957,44 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:51: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:39: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:63: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:61:15: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -3046,7 +4011,9 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o +[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp +[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, @@ -3068,10 +4035,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp +[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, @@ -3092,8 +4057,26 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M7::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:137:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:64:36: @@ -3142,8 +4125,78 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M8::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:150:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:64:36: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:65:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:31: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:52: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:64:36: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:65:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:31: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:52: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, @@ -3164,6 +4217,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:17: @@ -3188,43 +4243,40 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Utils/MapTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:147:52: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:153:59: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'virtual void bpp::YNGP_M9::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:150:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45, @@ -3280,86 +4332,101 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:38: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41: + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45, + from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: + inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:66:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: + inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:66:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:129:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:129:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, const bpp::SiteContainer&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:99:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, const std::vector >&, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:98:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:300:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:73:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:310:18: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, const bpp::SiteContainer&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:99:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'virtual void bpp::FullCodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:143:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::Tree&, bpp::TransitionModel*, bpp::DiscreteDistribution*, bool, bool, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:73:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, const std::vector >&, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:98:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp +[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h:46, @@ -3370,118 +4437,160 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void bpp::MvaFrequenciesSet::updateFrequencies()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:96:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp -[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:170:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:170:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o +[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp +[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, + from /usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h:46, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void bpp::MvaFrequenciesSet::updateFrequencies()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:96:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat 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-Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp -[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o +[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp +[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp +[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp +[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40: + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:730:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'virtual void bpp::MixtureOfASubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:266:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(const bpp::Node*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:737:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp -[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp -[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:109:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:109:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:74:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:75:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:74:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:75:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -3497,12 +4606,36 @@ | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:150:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:151:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void bpp::MixtureOfASubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:266:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:150:23: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:151:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -3513,6 +4646,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: @@ -3525,8 +4660,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -3572,6 +4705,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:150:23: @@ -3584,53 +4719,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o +[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:176:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:176:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -3682,8 +4772,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp +[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -3735,24 +4825,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -3761,15 +4835,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:460:17: + inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:449:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3778,7 +4852,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:461:17: + inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:450:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3787,7 +4861,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:462:17: + inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:451:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3796,7 +4870,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:463:17: + inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:452:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3804,14 +4878,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp -[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionMethods.cpp -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -3820,15 +4886,17 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:36: + inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:130:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3837,7 +4905,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:45: + inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:131:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3845,29 +4913,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:39: + inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:132:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3876,7 +4923,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:50: + inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:133:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3884,6 +4931,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -3892,51 +4941,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:39: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:50: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:63: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:74: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:85: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:460:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3945,7 +4958,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:96: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:461:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3954,7 +4967,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:38: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:462:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3963,7 +4976,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:50: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:463:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3971,8 +4984,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:61: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:460:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3981,7 +5013,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:38: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:461:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3990,7 +5022,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:50: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:462:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3999,7 +5031,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:61: + inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:463:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4007,10 +5039,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp -[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp +[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp +[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -4019,15 +5051,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::SSR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:112:17: + inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:36: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4036,7 +5068,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::SSR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:113:17: + inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:45: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4044,10 +5076,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp +[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -4056,33 +5090,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:22: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:33: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:46: + inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:36: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4091,7 +5107,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:57: + inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:45: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4099,8 +5115,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:68: + inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:39: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4109,7 +5142,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:79: + inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4117,10 +5150,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -4129,15 +5158,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:432:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:39: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4146,7 +5175,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:433:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4155,7 +5184,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:434:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:63: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4164,548 +5193,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:435:17: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.h:46, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp:41: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void bpp::Coala::computeEquilibriumFrequencies()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp:132:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, - from /usr/include/Bpp/Numeric/Function/Functions.h:45, - from /usr/include/Bpp/Numeric/NumTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:93:25: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:97:20: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:68:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:69:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:68:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:69:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/Mapping.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp -[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:64:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:65:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:65:21: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:66:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp -[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RE08.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:98:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:99:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:80:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:81:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:80:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:81:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp -[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp -[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45: -/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::AbstractSubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:144:31: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::AbstractSubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:145:32: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:414:34: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:74: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4714,7 +5202,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:422:76: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:85: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4723,7 +5211,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:422:46: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:96: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4732,7 +5220,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:428:34: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:38: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4741,7 +5229,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:442:36: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4750,7 +5238,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:446:76: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:61: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4759,7 +5247,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::AbstractWordSubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:446:46: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:38: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4767,62 +5255,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp -[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TopologySearch.h:48, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 133 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp: In member function 'void bpp::NNITopologySearch::searchPhyML()': -/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:290:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 290 | improvement.insert(improvement.begin() + static_cast(pos), diff); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 296 | improvement.insert(improvement.end(), diff); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void bpp::NNITopologySearch::searchBetter()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:188:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::BinarySubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:238:19: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4831,7 +5265,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::BinarySubstitutionModel::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:238:30: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:61: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4839,936 +5273,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp -[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp -[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp -[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp -[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp -[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp -[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp -[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp -[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Tree.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp:104:25: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp -[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void bpp::MutationPath::addEvent(size_t, double)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.h:125:23, - inlined from 'virtual bpp::MutationPath bpp::AbstractMutationProcess::detailedEvolve(size_t, double) const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp:114:16: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp -[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp -[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /usr/include/Bpp/Seq/SymbolList.h:43, - from /usr/include/Bpp/Seq/Site.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SiteSimulator.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp -[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = bpp::MutationPath; _Alloc = std::allocator]', - inlined from 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:121:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp:42: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp:517:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) 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libbpp-phyl.a -[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 70%] Built target bpp-phyl-static -[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/GY94.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KCM.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp -[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/MG94.cpp -[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp -[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43, - from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:115:22: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:116:27: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::SENCA::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp:120:22: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YN98.cpp -[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp -[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M1::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:135:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M1::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:136:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:59:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M1::YNGP_M1(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:60:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M10::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:151:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M10::YNGP_M10(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:72:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:140:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:141:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M2::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:142:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:51: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:39: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:63: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:58:51: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:39: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M2::YNGP_M2(const bpp::GeneticCode*, bpp::FrequenciesSet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:59:63: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M3::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:182:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:61:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:64:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:69:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:61:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:64:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M3::YNGP_M3(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:69:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M7::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:137:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp -[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M8::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:150:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:64:36: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:65:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:31: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:52: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:64:36: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:65:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:31: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M8::YNGP_M8(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:70:52: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::YNGP_M9::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:150:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::YNGP_M9::YNGP_M9(const bpp::GeneticCode*, bpp::FrequenciesSet*, unsigned int, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:72:38: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:66:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:66:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, const std::vector >&, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:98:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:300:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:310:18: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::FullCodonFrequenciesSet::setFrequencies(const std::vector >&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:143:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, const std::vector >&, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:98:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const std::string&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:104:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h:46, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void bpp::MvaFrequenciesSet::updateFrequencies()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:96:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp -[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp -[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp -[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp -[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'virtual void bpp::MixtureOfASubstitutionModel::updateMatrices()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:266:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:109:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:108:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfASubstitutionModel::MixtureOfASubstitutionModel(const bpp::Alphabet*, bpp::SubstitutionModel*, std::map, bpp::DiscreteDistribution*>, int, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:109:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:74:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:75:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:74:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:75:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:150:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:151:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:150:23: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const bpp::Alphabet*, std::vector, bpp::Vdouble&, bpp::Vdouble&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:151:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp -[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -5777,15 +5285,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:449:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:39: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5794,7 +5302,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:450:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5803,7 +5311,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:451:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:63: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5812,7 +5320,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::F84::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:452:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:74: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5820,25 +5328,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:130:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:85: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5847,7 +5338,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:131:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:96: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5856,7 +5347,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:132:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:38: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5865,7 +5356,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::GTR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:133:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5873,23 +5364,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:460:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:61: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5898,7 +5374,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:461:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:38: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5907,7 +5383,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:462:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5916,7 +5392,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::HKY85::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:463:17: + inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:61: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5924,12 +5400,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp -[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp -[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -5938,15 +5408,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:36: + inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:39: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5955,7 +5425,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::L95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:115:45: + inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:50: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5963,10 +5433,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp -[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp +[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp +[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -5975,51 +5445,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:39: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:50: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:63: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:74: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:85: + inlined from 'virtual void bpp::SSR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:112:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6028,7 +5462,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:524:96: + inlined from 'virtual void bpp::SSR::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:113:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6036,8 +5470,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:38: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:22: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6046,7 +5497,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:50: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:33: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6055,7 +5506,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:525:61: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:46: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6064,7 +5515,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:38: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:57: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6073,7 +5524,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:50: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:68: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6082,7 +5533,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:526:61: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:79: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6090,8 +5541,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -6125,8 +5576,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -6135,15 +5586,15 @@ from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40: + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:39: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:22: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6152,7 +5603,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::RN95s::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:474:50: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:33: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6160,25 +5611,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.h:43, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:22: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:46: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6187,7 +5621,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:33: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:57: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6196,7 +5630,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:46: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:68: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6205,7 +5639,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:57: + inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:79: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6213,8 +5647,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/../StateMap.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:68: + inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:432:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6223,7 +5674,7 @@ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'virtual void bpp::T92::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:460:79: + inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:433:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6231,7 +5682,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:434:17: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'virtual void bpp::TN93::setFreq(std::map&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:435:17: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, @@ -6284,25 +5753,42 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o +[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp -[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o +[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp +[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp +[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp -[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o +[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp -[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o +[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp +[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.h:46, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp:41: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void bpp::Coala::computeEquilibriumFrequencies()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp:132:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, - from /usr/include/Bpp/Numeric/Function/Functions.h:45, - from /usr/include/Bpp/Numeric/NumTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/../StateMap.h:44, @@ -6321,6 +5807,21 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, + from /usr/include/Bpp/Numeric/Function/Functions.h:45, + from /usr/include/Bpp/Numeric/NumTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:93:25: @@ -6340,19 +5841,93 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp -[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp -[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o +In file included from /usr/include/c++/12/map:60, + from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, + from /usr/include/Bpp/Numeric/Function/Functions.h:45, + from /usr/include/Bpp/Numeric/NumTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:93:25: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:97:20: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp -[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp +[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp -[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o +[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp +[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp -[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o +[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp +[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp -[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o +[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:68:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:69:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:68:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LG10_EX_EHO::LG10_EX_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:69:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, @@ -6390,6 +5965,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -6424,10 +6001,76 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp -[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LGL08_CAT::LGL08_CAT(const bpp::ProteicAlphabet*, unsigned int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EHO::LLG08_EHO(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -6462,6 +6105,12 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp +[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp +[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -6496,12 +6145,48 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o +[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX2::LLG08_EX2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -6532,12 +6217,80 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o +[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp -[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_EX3::LLG08_EX3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:64:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL2::LLG08_UL2(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:65:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp -[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -6572,7 +6325,45 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:65:21: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'bpp::LLG08_UL3::LLG08_UL3(const bpp::ProteicAlphabet*)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:66:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RE08.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, @@ -6608,22 +6399,38 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp +[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp -[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o +[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp -[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o +[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp +[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp +[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp +[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp -[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o +[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp +[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp +[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp In file included from /usr/include/c++/12/vector:70, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TopologySearch.h:48, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.h:43, @@ -6645,8 +6452,43 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o +/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp: In member function 'void bpp::NNITopologySearch::searchPhyML()': +/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:290:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 290 | improvement.insert(improvement.begin() + static_cast(pos), diff); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 296 | improvement.insert(improvement.end(), diff); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void bpp::NNITopologySearch::searchBetter()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:188:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp +[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TopologySearch.h:48, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 133 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp: In member function 'void bpp::NNITopologySearch::searchPhyML()': /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:290:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 290 | improvement.insert(improvement.begin() + static_cast(pos), diff); @@ -6654,12 +6496,33 @@ /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:31: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 296 | improvement.insert(improvement.end(), diff); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bpp::NNITopologySearch::searchBetter()' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:188:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -6678,8 +6541,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -6698,12 +6561,36 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp +[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp +[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp +[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp +[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, @@ -6725,7 +6612,27 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp +[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, @@ -6746,6 +6653,31 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Tree.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp:104:25: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp +[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp +In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/../StateMap.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:44, @@ -6763,16 +6695,61 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/../StateMap.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void bpp::MutationPath::addEvent(size_t, double)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.h:125:23, + inlined from 'virtual bpp::MutationPath bpp::AbstractMutationProcess::detailedEvolve(size_t, double) const' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp:114:16: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /usr/include/Bpp/Seq/SymbolList.h:43, + from /usr/include/Bpp/Seq/Site.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SiteSimulator.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp -[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = bpp::MutationPath; _Alloc = std::allocator]', + inlined from 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:121:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/SymbolList.h:43, @@ -6791,6 +6768,12 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp +[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -6800,6 +6783,10 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp +[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, @@ -6833,6 +6820,27 @@ from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.h:45, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp:42: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp:517:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -6844,14 +6852,46 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static bpp::Vdouble bpp::TreeTools::getBranchLengths(const bpp::Tree&, int)' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp:484:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.h:43, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 92%] Linking CXX shared library libbpp-phyl.so cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-phyl.so.12 -o libbpp-phyl.so.12.0.0 "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o" 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"CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o" cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl.so.12.0.0 libbpp-phyl.so.12 libbpp-phyl.so make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [ 92%] Built target bpp-phyl-shared @@ -6865,25 +6905,38 @@ make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_bowker.cpp -[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 93%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o +[ 93%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood.cpp -[ 94%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp +[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_bowker.cpp +/usr/bin/ranlib libbpp-phyl.a +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 94%] Built target bpp-phyl-static +make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_clock.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, - from /usr/include/Bpp/Seq/Alphabet/DNA.h:44, - from /build/libbpp-phyl-2.4.1/test/test_bowker.cpp:40: + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43, + from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43, + from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43, + from /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -6894,18 +6947,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43, - from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43, - from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43, - from /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp:40: + from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, + from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, + from /usr/include/Bpp/Seq/Alphabet/DNA.h:44, + from /build/libbpp-phyl-2.4.1/test/test_bowker.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -6916,6 +6962,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -6984,22 +7035,6 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [ 94%] Built target test_likelihood -make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_clock.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp -[ 94%] Linking CXX executable test_detailed_simulations -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 -[ 94%] Linking CXX executable test_bowker -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 94%] Built target test_detailed_simulations make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_mapping.dir/DependInfo.cmake --color= @@ -7008,29 +7043,71 @@ make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping.cpp +[ 94%] Linking CXX executable test_detailed_simulations +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 94%] Built target test_bowker +[ 94%] Built target test_detailed_simulations make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_mapping_codon.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 94%] Linking CXX executable test_bowker +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 [ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp -[ 95%] Linking CXX executable test_likelihood_clock -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 95%] Built target test_likelihood_clock +[ 94%] Built target test_bowker make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_models.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 95%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_models.dir/test_models.cpp.o -MF CMakeFiles/test_models.dir/test_models.cpp.o.d -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_models.cpp +[ 95%] Linking CXX executable test_likelihood_clock +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 95%] Built target test_likelihood_clock +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_nhx.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 95%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_nhx.cpp +[ 96%] Linking CXX executable test_nhx +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 96%] Built target test_nhx +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 96%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_parsimony.cpp +[ 96%] Linking CXX executable test_models +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 96%] Built target test_models +make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_simulations.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_simulations.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, @@ -7068,58 +7145,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 96%] Linking CXX executable test_mapping_codon -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Built target test_mapping_codon -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_nhx.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_nhx.cpp -[ 96%] Linking CXX executable test_mapping -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Built target test_mapping -make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_parsimony.cpp -[ 96%] Linking CXX executable test_models -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Built target test_models -make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_simulations.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_simulations.cpp -[ 98%] Linking CXX executable test_nhx -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 98%] Built target test_nhx -make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, @@ -7136,6 +7161,19 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 98%] Linking CXX executable test_mapping_codon +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 98%] Built target test_mapping_codon +make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 98%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree.cpp [ 98%] Linking CXX executable test_parsimony cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 @@ -7149,26 +7187,11 @@ make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [ 99%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Text/TextTools.h:49, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, - from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:44, - from /build/libbpp-phyl-2.4.1/test/test_tree.cpp:40: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 99%] Linking CXX executable test_tree -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[ 99%] Linking CXX executable test_mapping +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 99%] Built target test_tree +[ 99%] Built target test_mapping make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake --color= @@ -7206,6 +7229,21 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Text/TextTools.h:49, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, + from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:44, + from /build/libbpp-phyl-2.4.1/test/test_tree.cpp:40: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main()' at /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:76:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -7226,24 +7264,29 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 99%] Linking CXX executable test_simulations -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[ 99%] Linking CXX executable test_tree +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 99%] Built target test_simulations +[ 99%] Built target test_tree [100%] Linking CXX executable test_tree_rootat cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_rootat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[100%] Linking CXX executable test_simulations +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [100%] Built target test_tree_rootat +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[100%] Built target test_simulations make[2]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' dh_auto_test - cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 + cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j3 +/usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/DartConfiguration.tcl @@ -7273,10 +7316,19 @@ 3: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_likelihood 3: Working Directory: /build/libbpp-phyl-2.4.1/test 3: Test timeout computed to be: 60000 +test 4 + Start 4: test_likelihood_clock + +4: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_likelihood_clock +4: Working Directory: /build/libbpp-phyl-2.4.1/test +4: Test timeout computed to be: 60000 1: / 1 - 2 \ 3 nodes loaded. 1: ..:: Testing with homogeneous model ::.. 2: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 2: 4 +4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 3: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 3: Testing Single Tree Traversal likelihood class... 3: Initializing data structure............: Done. @@ -7284,6 +7336,10 @@ 3: Test model.............................: T92 3: 85.030942031950203841 3: * initial likelihood...................: 85.0309 +4: Test model.............................: T92 +4: 94.395699097704181213 +4: * initial likelihood...................: 94.3957 +4: Log-likelihood after adding clock......: 94.3957 3: Initial bracketing: 3: A: x = 0.5, f = 80.2872 3: B: x = 2.11803, f = 71.6905 @@ -7294,6 +7350,25 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 +4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 +4: +4: 71.26579958637299228 +4: * likelihood after full optimization...: 71.2658 +4: Name: Value: Constraint: +4: _________________________________________________ +4: BrLen0 0.143684 [ 1e-06; 10000] +4: BrLen1 0.143684 [ 1e-06; 10000] +4: BrLen2 0.031698 [ 1e-06; 10000] +4: BrLen3 0.175382 [ 1e-06; 10000] +4: BrLen4 0.272930 [ 1e-06; 10000] +4: BrLen5 0.448312 [ 1e-06; 10000] +4: T92.kappa 0.996464 ]0; +inf[ +4: T92.theta 0.579955 ]1e-06; 0.999999[ +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +4: Test model.............................: T92 +4: 92.32951163315719611546 +4: * initial likelihood...................: 92.3295 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215039306338 @@ -7314,52 +7389,6 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 -3: -3: 65.72293577215069149133 -3: * likelihood after full optimization...: 65.7229 -3: Initializing data structure............: Done. -3: Number of distinct sites...............: 12 -3: Initializing data structure............: Done. -3: Number of distinct sites...............: 12 -3: BrLen0 -212.54368339472844695592 -212.54368339472844695592 -3: BrLen1 -107.42239645667785907790 -107.42239645667787328875 -3: BrLen2 3.41183634475365238359 3.41183634475364838679 -3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 -3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 - 1/13 Test #3: test_likelihood .................. Passed 0.49 sec -test 4 - Start 4: test_likelihood_clock - -4: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_likelihood_clock -4: Working Directory: /build/libbpp-phyl-2.4.1/test -4: Test timeout computed to be: 60000 -4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 94.395699097704181213 -4: * initial likelihood...................: 94.3957 -4: Log-likelihood after adding clock......: 94.3957 -4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 -4: -4: 71.26579958637299228 -4: * likelihood after full optimization...: 71.2658 -4: Name: Value: Constraint: -4: _________________________________________________ -4: BrLen0 0.143684 [ 1e-06; 10000] -4: BrLen1 0.143684 [ 1e-06; 10000] -4: BrLen2 0.031698 [ 1e-06; 10000] -4: BrLen3 0.175382 [ 1e-06; 10000] -4: BrLen4 0.272930 [ 1e-06; 10000] -4: BrLen5 0.448312 [ 1e-06; 10000] -4: T92.kappa 0.996464 ]0; +inf[ -4: T92.theta 0.579955 ]1e-06; 0.999999[ -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 92.32951163315719611546 -4: * initial likelihood...................: 92.3295 4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 4: 4: 71.26579406919543657750 @@ -7371,7 +7400,7 @@ 4: HeightP2 0.819072 [ 0; 1] 4: T92.kappa 0.996398 ]0; +inf[ 4: T92.theta 0.579960 ]1e-06; 0.999999[ - 2/13 Test #4: test_likelihood_clock ............ Passed 0.23 sec + 1/13 Test #4: test_likelihood_clock ............ Passed 0.13 sec test 5 Start 5: test_mapping @@ -7386,10 +7415,31 @@ 5: [0.259067, 0.362694, -0.777202, 0.15544] 5: [0.0518135, 0.906736, 0.272021, -1.23057] 5: ] +3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 +3: +3: 65.72293577215069149133 +3: * likelihood after full optimization...: 65.7229 +3: Initializing data structure............: Done. +3: Number of distinct sites...............: 12 +3: Initializing data structure............: Done. +3: Number of distinct sites...............: 12 +3: BrLen0 -212.54368339472844695592 -212.54368339472844695592 +3: BrLen1 -107.42239645667785907790 -107.42239645667787328875 +3: BrLen2 3.41183634475365238359 3.41183634475364838679 +3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 +3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 + 2/13 Test #3: test_likelihood .................. Passed 0.25 sec +test 6 + Start 6: test_mapping_codon + +6: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_mapping_codon +6: Working Directory: /build/libbpp-phyl-2.4.1/test +6: Test timeout computed to be: 60000 +6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 5: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 78% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 5: Initializing data structure............: Done. -5: Number of distinct sites...............: 82 -5: 77515.7 +5: Number of distinct sites...............: 79 +5: 77270.8 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -7418,55 +7468,7 @@ 5: [0, 0, 0, 0] 5: [0, 0, 0, 0] 5: ] -2: Br0 BrLen = 0.001 counts = 0.00099 -2: 4x4 -2: [ -2: [0, 2e-05, 0.00013, 2e-05] -2: [3e-05, 0, 5e-05, 0.00021] -2: [0.00011, 9e-05, 0, 9e-05] -2: [0, 0.00019, 5e-05, 0] -2: ] -2: Br1 BrLen = 0.002 counts = 0.00157 -2: 4x4 -2: [ -2: [0, 6e-05, 0.00014, 0] -2: [7e-05, 0, 0.00021, 0.00032] -2: [0.00011, 0.00018, 0, 0.00011] -2: [2e-05, 0.00025, 0.0001, 0] -2: ] -2: Br2 BrLen = 0.003 counts = 0.00294 -2: 4x4 -2: [ -2: [0, 0.00012, 0.00023, 3e-05] -2: [0.0001, 0, 0.00036, 0.00058] -2: [0.00023, 0.0004, 0, 0.00019] -2: [4e-05, 0.00055, 0.00011, 0] -2: ] -2: Br3 BrLen = 0.01 counts = 0.01042 -2: 4x4 -2: [ -2: [0, 0.0004, 0.00106, 9e-05] -2: [0.00033, 0, 0.0014, 0.00178] -2: [0.00095, 0.00136, 0, 0.00065] -2: [0.00014, 0.00181, 0.00045, 0] -2: ] -2: Br4 BrLen = 0.1 counts = 0.09995 -2: 4x4 -2: [ -2: [0, 0.00379, 0.00862, 0.001] -2: [0.00357, 0, 0.01288, 0.01747] -2: [0.00931, 0.01313, 0, 0.00543] -2: [0.00114, 0.018, 0.00561, 0] -2: ] - 3/13 Test #2: test_detailed_simulations ........ Passed 5.02 sec -test 6 - Start 6: test_mapping_codon - -6: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_mapping_codon -6: Working Directory: /build/libbpp-phyl-2.4.1/test -6: Test timeout computed to be: 60000 5: Compute joint node-pairs likelihood....: -6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Total count, decomposition method: 5: 4x4 @@ -7486,6 +7488,53 @@ 5: [6.26537e-09, 0.000129478, 5.67996e-12, 5.21646e-08] 5: [6.26139e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12] 5: ] +2: Br0 BrLen = 0.001 counts = 0.00094 +2: 4x4 +2: [ +2: [0, 4e-05, 0.0001, 2e-05] +2: [4e-05, 0, 9e-05, 0.00011] +2: [9e-05, 0.00017, 0, 7e-05] +2: [1e-05, 0.00018, 2e-05, 0] +2: ] +2: Br1 BrLen = 0.002 counts = 0.00215 +2: 4x4 +2: [ +2: [0, 1e-05, 0.00025, 1e-05] +2: [7e-05, 0, 0.00036, 0.0004] +2: [0.00014, 0.00029, 0, 0.00015] +2: [1e-05, 0.00035, 0.00011, 0] +2: ] +2: Br2 BrLen = 0.003 counts = 0.00304 +2: 4x4 +2: [ +2: [0, 0.00015, 0.00024, 5e-05] +2: [0.0001, 0, 0.0004, 0.00054] +2: [0.00029, 0.00036, 0, 0.00015] +2: [3e-05, 0.00062, 0.00011, 0] +2: ] +2: Br3 BrLen = 0.01 counts = 0.00945 +2: 4x4 +2: [ +2: [0, 0.00025, 0.00083, 4e-05] +2: [0.00033, 0, 0.00134, 0.00174] +2: [0.0009, 0.00121, 0, 0.00046] +2: [0.00014, 0.00172, 0.00049, 0] +2: ] +2: Br4 BrLen = 0.1 counts = 0.09966 +2: 4x4 +2: [ +2: [0, 0.00343, 0.00934, 0.00112] +2: [0.00329, 0, 0.01288, 0.01768] +2: [0.00926, 0.01306, 0, 0.0053] +2: [0.00103, 0.01807, 0.0052, 0] +2: ] + 3/13 Test #2: test_detailed_simulations ........ Passed 2.73 sec +test 7 + Start 7: test_models + +7: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_models +7: Working Directory: /build/libbpp-phyl-2.4.1/test +7: Test timeout computed to be: 60000 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Total count, uniformization method: @@ -7496,7 +7545,21 @@ 5: [1.00009, 1.00032, 4.08766e-07, 1.00069] 5: [1.00159, 1.00007, 1.00069, 5.17576e-07] 5: ] + 4/13 Test #7: test_models ...................... Passed 0.14 sec +test 8 + Start 8: test_nhx + +8: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_nhx +8: Working Directory: /build/libbpp-phyl-2.4.1/test +8: Test timeout computed to be: 60000 5: Compute joint node-pairs likelihood....: + 5/13 Test #8: test_nhx ......................... Passed 0.03 sec +test 9 + Start 9: test_parsimony + +9: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_parsimony +9: Working Directory: /build/libbpp-phyl-2.4.1/test +9: Test timeout computed to be: 60000 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, uniformization method, type 1: 5: 4x4 @@ -7506,6 +7569,23 @@ 5: [6.26538e-09, 0.000129478, 5.67996e-12, 5.21646e-08] 5: [6.2614e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12] 5: ] +9: Initializing data structure............: Done. +9: Number of distinct sites...............: 9 +9: Parsimony score: 9 + 6/13 Test #9: test_parsimony ................... Passed 0.03 sec +test 10 + Start 10: test_simulations + +10: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_simulations +10: Working Directory: /build/libbpp-phyl-2.4.1/test +10: Test timeout computed to be: 60000 +10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +10: Theta0 set to 0.622444 +10: Theta1 set to 0.822305 +10: Theta2 set to 0.850304 +10: Theta3 set to 0.861762 +10: Theta4 set to 0.393673 +10: Fast check: 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: checking saturation... @@ -7581,66 +7661,122 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 55 52.6358 52.5964 52.5964 52.6358 52.6358 52.6358 52.6358 -5: B 0.002 102 104.66 104.504 104.504 104.66 104.66 104.66 104.66 -5: 0.008 389 388.967 386.576 386.576 388.967 388.967 388.967 388.967 -5: C 0.01 543 540.835 536.848 536.848 540.835 540.835 540.835 540.835 -5: D 0.02 1051 1044.75 1029.18 1029.18 1044.75 1044.75 1044.75 1044.75 -5: A 0.001 3.00206/3 3.00363/3 3.00363/3 3.01876/3 3.02381/3 3.02381/3 0.999628/1 0.998711/1 0.998711/1 1.99168/2 1.9929/2 1.9929/2 -5: B 0.002 7.00993/7 7.01169/7 7.01169/7 8.83437/7 8.85769/7 8.85769/7 2.00131/2 1.99811/2 1.99811/2 3.99958/4 4.0046/4 4.0046/4 -5: 0.008 12.6951/12 12.7633/12 12.7633/12 40.0792/40 40.3366/40 40.3366/40 2.0744/2 2.08796/2 2.08796/2 16.4413/16 16.4863/16 16.4863/16 -5: C 0.01 21.5893/21 21.6746/21 21.6746/21 49.0749/48 49.5221/48 49.5221/48 4.19665/4 4.20945/4 4.20945/4 29.9553/30 30.009/30 30.009/30 -5: D 0.02 34.7067/37 35.1165/37 35.1165/37 81.8005/82 83.5898/82 83.5898/82 8.69006/8 8.69708/8 8.69708/8 33.476/35 33.9941/35 33.9941/35 - 4/13 Test #5: test_mapping ..................... Passed 7.28 sec -test 7 - Start 7: test_models - -7: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_models -7: Working Directory: /build/libbpp-phyl-2.4.1/test -7: Test timeout computed to be: 60000 - 5/13 Test #7: test_models ...................... Passed 0.27 sec -test 8 - Start 8: test_nhx +5: A 0.001 49 45.1515 45.1189 45.1189 45.1515 45.1515 45.1515 45.1515 +5: B 0.002 105 106.139 105.983 105.983 106.139 106.139 106.139 106.139 +5: 0.008 405 409.823 407.279 407.279 409.823 409.823 409.823 409.823 +5: C 0.01 499 495.573 491.658 491.658 495.573 495.573 495.573 495.573 +5: D 0.02 995 996.389 981.256 981.256 996.389 996.389 996.389 996.389 +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 191 +5: A 0.001 1.00432/1 1.00486/1 1.00486/1 5.02917/5 5.03273/5 5.03273/5 0.000219288/0 0.000719031/0 0.000719031/0 0.997999/1 0.999088/1 0.999088/1 +5: B 0.002 5.00358/5 5.00837/5 5.00837/5 12.7631/11 12.7828/11 12.7828/11 1.99979/2 1.9967/2 1.9967/2 2.99776/3 3.0008/3 3.0008/3 +5: 0.008 17.3914/16 17.4871/16 17.4871/16 41.5214/40 41.8242/40 41.8242/40 8.21423/8 8.15906/8 8.15906/8 18.9592/18 19.0148/18 19.0148/18 +5: C 0.01 15.7241/16 15.8496/16 15.8496/16 41.631/40 42.0805/40 42.0805/40 6.01499/6 5.98455/6 5.98455/6 22.3092/23 22.4113/23 22.4113/23 +5: D 0.02 34.9496/37 35.4663/37 35.4663/37 86.4046/86 88.239/86 88.239/86 15.3571/15 15.1222/15 15.1222/15 39.2178/39 39.5701/39 39.5701/39 + 7/13 Test #5: test_mapping ..................... Passed 4.56 sec +test 11 + Start 11: test_tree -8: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_nhx -8: Working Directory: /build/libbpp-phyl-2.4.1/test -8: Test timeout computed to be: 60000 - 6/13 Test #8: test_nhx ......................... Passed 0.06 sec -test 9 - Start 9: test_parsimony +11: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree +11: Working Directory: /build/libbpp-phyl-2.4.1/test +11: Test timeout computed to be: 60000 +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4); +11: +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A,B),C); +11: +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A:1,B:2)80:3,C:4):5; +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: N: BOOTSTRAP=80 +11: Node 3: +11: Node 4: +11: N: BOOTSTRAP=2 +11: ((A,B),C); +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: B: ESS=aa +11: Node 3: +11: Node 4: +11: B: ESS=2 +11: Newick I/O ok. +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0393 0.0055 +1: ..:: Testing with homogeneous, non-stationary model ::.. +11: Newick multiple I/O ok. +11: Testing parsing a directory... +11: Ok, reading on directory throws exception! +11: Testing parsing a directory for multiple trees... +11: Error, no exception should be thrown here! +11: Testing a tree with a node of degree 2: +11: / 1 - 2 \ 3 - 4 nodes loaded. +11: ((A:1):2,B); +11: +11: Testing a tree with a node of degree 2, without branch length: +11: / 1 - 2 \ 3 - 4 nodes loaded. +11: ((A),B); +11: +11: Testing a tree with several single nodes: +11: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 - 8 nodes loaded. +11: ((((((A)):1)):3),B); +11: +11: Testing a tree with a single leaf: +11: / 1 - 2 nodes loaded. +11: (A:1); +11: +11: Testing a tree with a single node: +11: / 1 - 2 \ 3 nodes loaded. +11: ((A:1)); +11: +11: Testing a tree with a single node and branch lengths: +11: / 1 - 2 \ 3 nodes loaded. +11: ((A:1):2); +11: + 8/13 Test #11: test_tree ........................ Passed 11.24 sec +test 12 + Start 12: test_tree_getpath -9: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_parsimony -9: Working Directory: /build/libbpp-phyl-2.4.1/test -9: Test timeout computed to be: 60000 -9: Initializing data structure............: Done. -9: Number of distinct sites...............: 9 -9: Parsimony score: 9 - 7/13 Test #9: test_parsimony ................... Passed 0.06 sec -test 10 - Start 10: test_simulations +12: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree_getpath +12: Working Directory: /build/libbpp-phyl-2.4.1/test +12: Test timeout computed to be: 60000 +12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +12: Id node1 0 +12: Id node2 1 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 1 +12: Id node1 0 +12: Id node3 2 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 2 + 9/13 Test #12: test_tree_getpath ................ Passed 0.03 sec +test 13 + Start 13: test_tree_rootat -10: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_simulations -10: Working Directory: /build/libbpp-phyl-2.4.1/test -10: Test timeout computed to be: 60000 -10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.660038 -10: Theta1 set to 0.608461 -10: Theta2 set to 0.0323224 -10: Theta3 set to 0.0650041 -10: Theta4 set to 0.529584 -10: Fast check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 197 -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0407 0.0054 -1: ..:: Testing with homogeneous, non-stationary model ::.. -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0391 0.0049 +13: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree_rootat +13: Working Directory: /build/libbpp-phyl-2.4.1/test +13: Test timeout computed to be: 60000 +13: Total length...........................: 100.253 +10/13 Test #13: test_tree_rootat ................. Passed 0.34 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0401 0.0061 1: ..:: Testing with non-homogeneous, non-stationary model ::.. -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9351 0.8073 -1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 79% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 6: Initializing data structure............: Done. -6: Number of distinct sites...............: 1045 -6: 96754.9 +6: Number of distinct sites...............: 1004 +6: 96365 6: Analytical total count: 6: 64x64 6: [ @@ -7710,6 +7846,8 @@ 6: [3.00169, 3.00145, 3.00139, 2.00023, 3.00149, 3.00181, 3.00139, 2.00023, 3.00136, 3.0016, 3.00152, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00144, 3.0014, 3.00135, 2.00023, 3.00092, 3.00161, 3.00111, 2.00023, 3.00164, 3.00171, 3.0018, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00157, 3.00128, 3.00143, 2.00023, 3.00155, 3.0017, 3.00158, 2.00023, 3.00136, 3.0013, 3.00154, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, nan, 2.00015, nan, 1.00012, 2.00015, 2.00023, 2.00019, 1.00012, nan, 2.00019, 2.00015, 1.00012, 1.00012, 1.00012, 1.00012, 1.21058e-07] 6: ] 6: Compute joint node-pairs likelihood....: +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9315 0.7972 +1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: 6: 64x64 @@ -7850,6 +7988,14 @@ 6: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0] 6: ] 6: Compute joint node-pairs likelihood....: +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 +10: +10: 0.622444 0.618322 +10: 0.822305 0.807897 +10: 0.850304 0.841356 +10: 0.861762 0.842873 +10: 0.393673 0.390894 +10: Detailed check: 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Total count, uniformization method: 6: 64x64 @@ -7920,14 +8066,6 @@ 6: [3.00046, 3.00008, 3.00018, 2.00023, 3.00012, 3.00044, 3.00002, 2.00023, 3.00015, 3.00023, 3.00015, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00021, 3.00003, 3.00014, 2.00023, 2.99955, 3.00024, 2.99974, 2.00023, 3.00043, 3.00034, 3.00043, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00034, 2.99991, 3.00022, 2.00023, 3.00018, 3.00033, 3.00021, 2.00023, 3.00015, 2.99993, 3.00017, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 0, 2.00015, 0, 1.00012, 2.00015, 2.00023, 2.00019, 1.00012, 0, 2.00019, 2.00015, 1.00012, 1.00012, 1.00012, 1.00012, 1.21058e-07] 6: ] 6: Compute joint node-pairs likelihood....: -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0398 0.0065 - 8/13 Test #1: test_bowker ...................... Passed 58.41 sec -test 11 - Start 11: test_tree - -11: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree -11: Working Directory: /build/libbpp-phyl-2.4.1/test -11: Test timeout computed to be: 60000 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Detailed count, uniformization method, type 2: 6: 64x64 @@ -7998,124 +8136,29 @@ 6: [2.75035, 2.00021, 3, 2.00023, 2.3334, 2.00039, 2.49994, 2.00023, 2.74999, 2.00034, 2.99996, 2.00023, 1.50015, 1.00029, 2.00008, 1.00012, 2.50014, 2.00014, 2.50011, 2.00023, 2.16633, 2.00021, 2.16649, 2.00023, 2.00034, 2.0003, 2.33363, 2.00023, 1.00015, 1.00019, 1.00017, 1.00012, 2.75019, 2.00008, 2.7501, 2.00023, 2.33341, 2.0003, 2.33346, 2.00023, 2.2501, 2.00005, 2.50008, 2.00023, 1.5001, 1.00023, 1.50011, 1.00012, 0, 1.00019, 0, 1.00012, 1.50004, 1.00023, 1.50009, 1.00012, 0, 1.00027, 2.00006, 1.00012, 1, 0.000232033, 1, 1.07607e-07] 6: ] 6: Compute joint node-pairs likelihood....: -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4); -11: -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A,B),C); -11: -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A:1,B:2)80:3,C:4):5; -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: N: BOOTSTRAP=80 -11: Node 3: -11: Node 4: -11: N: BOOTSTRAP=2 -11: ((A,B),C); -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: B: ESS=aa -11: Node 3: -11: Node 4: -11: B: ESS=2 -6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -11: Newick I/O ok. - 9/13 Test #6: test_mapping_codon ............... Passed 58.72 sec -test 12 - Start 12: test_tree_getpath - -12: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree_getpath -12: Working Directory: /build/libbpp-phyl-2.4.1/test -12: Test timeout computed to be: 60000 -12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -12: Id node1 0 -12: Id node2 1 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 1 -12: Id node1 0 -12: Id node3 2 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 2 -10/13 Test #12: test_tree_getpath ................ Passed 0.05 sec -test 13 - Start 13: test_tree_rootat - -13: Test command: /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test/test_tree_rootat -13: Working Directory: /build/libbpp-phyl-2.4.1/test -13: Test timeout computed to be: 60000 -13: Total length...........................: 93.7565 -11/13 Test #13: test_tree_rootat ................. Passed 0.69 sec -11: Newick multiple I/O ok. -11: Testing parsing a directory... -11: Ok, reading on directory throws exception! -11: Testing parsing a directory for multiple trees... -11: Error, no exception should be thrown here! -11: Testing a tree with a node of degree 2: -11: / 1 - 2 \ 3 - 4 nodes loaded. -11: ((A:1):2,B); -11: -11: Testing a tree with a node of degree 2, without branch length: -11: / 1 - 2 \ 3 - 4 nodes loaded. -11: ((A),B); -11: -11: Testing a tree with several single nodes: -11: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 - 8 nodes loaded. -11: ((((((A)):1)):3),B); -11: -11: Testing a tree with a single leaf: -11: / 1 - 2 nodes loaded. -11: (A:1); -11: -11: Testing a tree with a single node: -11: / 1 - 2 \ 3 nodes loaded. -11: ((A:1)); -11: -11: Testing a tree with a single node and branch lengths: -11: / 1 - 2 \ 3 nodes loaded. -11: ((A:1):2); -11: -12/13 Test #11: test_tree ........................ Passed 16.79 sec -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 Optimizing... - 56 Optimizing... / 57 Optimizing... - 58 Optimizing... \ 59 Optimizing... - 60 Optimizing... / 61 Optimizing... - 62 Optimizing... \ 63 Optimizing... - 64 Optimizing... / 65 Optimizing... - 66 Optimizing... \ 67 Optimizing... - 68 Optimizing... / 69 Optimizing... - 70 Optimizing... \ 71 Optimizing... - 72 Optimizing... / 73 Optimizing... - 74 Optimizing... \ 75 Optimizing... - 76 Optimizing... / 77 Optimizing... - 78 Optimizing... \ 79 Optimizing... - 80 Optimizing... / 81 Optimizing... - 82 Optimizing... \ 83 Optimizing... - 84 Optimizing... / 85 Optimizing... - 86 Optimizing... \ 87 Optimizing... - 88 Optimizing... / 89 Optimizing... - 90 Optimizing... \ 91 Optimizing... - 92 Optimizing... / 93 Optimizing... - 94 Optimizing... \ 95 Optimizing... - 96 Optimizing... / 97 Optimizing... - 98 Optimizing... \ 99 Optimizing... - 100 Optimizing... / 101 Optimizing... - 102 Optimizing... \ 103 Optimizing... - 104 Optimizing... / 105 Optimizing... - 106 Optimizing... \ 107 Optimizing... - 108 Optimizing... / 109 Optimizing... - 110 Optimizing... \ 111 Optimizing... - 112 Optimizing... / 113 Optimizing... - 114 Optimizing... \ 115 Optimizing... - 116 Optimizing... / 117 Optimizing... - 118 Optimizing... \ 119 Optimizing... - 120 Optimizing... / 121 Optimizing... - 122 Optimizing... \ 123 Optimizing... - 124 Optimizing... / 125 Optimizing... - 126 Optimizing... \ 127 Optimizing... - 128 Optimizing... / 129 Optimizing... - 130 Optimizing... \ 131 Optimizing... - 132 Optimizing... / 133 Optimizing... - 134 Optimizing... \ 135 Optimizing... - 136 Optimizing... / 137 Optimizing... - 138 Optimizing... \ 139 Optimizing... - 140 Optimizing... / 141 Optimizing... - 142 Optimizing... \ 143 Optimizing... - 144 Optimizing... / 145 Optimizing... - 146 Optimizing... \ 147 Optimizing... - 148 Optimizing... / 149 Optimizing... - 150 Optimizing... \ 151 Optimizing... - 152 Optimizing... / 153 Optimizing... - 154 Optimizing... \ 155 Optimizing... - 156 Optimizing... / 157 Optimizing... - 158 Optimizing... \ 159 Optimizing... - 160 Optimizing... / 161 Optimizing... - 162 Optimizing... \ 163 Optimizing... - 164 Optimizing... / 165 Optimizing... - 166 Optimizing... \ 167 Optimizing... - 168 Optimizing... / 169 Optimizing... - 170 Optimizing... \ 171 Optimizing... - 172 Optimizing... / 173 Optimizing... - 174 Optimizing... \ 175 Optimizing... - 176 Optimizing... / 177 Optimizing... - 178 Optimizing... \ 179 -10: -10: 0.660038 0.662276 -10: 0.608461 0.604268 -10: 0.0323224 0.0338388 -10: 0.0650041 0.0538467 -10: 0.529584 0.52517 -10: Detailed check: 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 195 -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 +10: Number of distinct sites...............: 190 +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0408 0.0065 +11/13 Test #1: test_bowker ...................... Passed 36.08 sec +6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. +12/13 Test #6: test_mapping_codon ............... Passed 36.20 sec +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 10: -10: 0.660038 0.653034 -10: 0.608461 0.601132 -10: 0.0323224 0.0366948 -10: 0.0650041 0.0876603 -10: 0.529584 0.540396 -13/13 Test #10: test_simulations ................. Passed 398.00 sec +10: 0.622444 0.627301 +10: 0.822305 0.81644 +10: 0.850304 0.837105 +10: 0.861762 0.854461 +10: 0.393673 0.394512 +13/13 Test #10: test_simulations ................. Passed 56.29 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 406.42 sec +Total Test time (real) = 59.25 sec make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-phyl-2.4.1 -B/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -8133,237 +8176,237 @@ -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/OptimizationTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/InMixedSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWrappedModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/InMixedSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/CoalaCore.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JCprot.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WrappedModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeTransitionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWrappedModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeTransitionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/MG94.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M2.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WrappedModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h --- 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/build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Tree.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h -- 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/build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h --- Installing: 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/build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RASTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/AncestralStateReconstruction.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionReward.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionMethods.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Mapping.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Mapping.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Reward.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionReward.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionMethods.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNITopologySearch.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets.cmake -- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets-none.cmake make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' @@ -8411,8 +8454,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl12' in '../libbpp-phyl12_2.4.1-8_armhf.deb'. dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-8_armhf.deb'. +dpkg-deb: building package 'libbpp-phyl12' in '../libbpp-phyl12_2.4.1-8_armhf.deb'. dpkg-deb: building package 'libbpp-phyl12-dbgsym' in '../libbpp-phyl12-dbgsym_2.4.1-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-8_armhf.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-8_armhf.changes @@ -8421,12 +8464,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/13264/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13264/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/6221 and its subdirectories -I: Current time: Mon Jun 5 13:59:05 -12 2023 -I: pbuilder-time-stamp: 1686016745 +I: removing directory /srv/workspace/pbuilder/13264 and its subdirectories +I: Current time: Tue Jun 6 16:35:35 +14 2023 +I: pbuilder-time-stamp: 1686018935