Diff of the two buildlogs: -- --- b1/build.log 2020-06-09 01:58:47.031755951 +0000 +++ b2/build.log 2020-06-09 02:37:34.742306580 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 8 10:54:04 -12 2020 -I: pbuilder-time-stamp: 1591656844 +I: Current time: Tue Jun 9 16:00:03 +14 2020 +I: pbuilder-time-stamp: 1591668003 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 1 05:21:34 2019 -12 +gpgv: Signature made Sat Mar 2 07:21:34 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying increase_test_tolerance.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/13564/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21847/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/21847/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21847/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='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.0.3(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=6' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='14d19d87baa44b7f9dc3196ac4dd3772' - 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='13564' - PS1='# ' - PS2='> ' + INVOCATION_ID=5060df440bb34757b2805662430c2bf4 + 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=21847 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.1zX1Rjy3RX/pbuilderrc_QwlV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1zX1Rjy3RX/b1 --logfile b1/build.log libbpp-phyl_2.4.1-2.dsc' - SUDO_GID='116' - SUDO_UID='112' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.1zX1Rjy3RX/pbuilderrc_ihau --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1zX1Rjy3RX/b2 --logfile b2/build.log libbpp-phyl_2.4.1-2.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux cbxi4b 4.19.0-9-armmp #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2 (2020-04-29) aarch64 GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 20:27 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/13564/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 9 16:00 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 8 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/21847/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -264,7 +298,7 @@ Get: 61 http://deb.debian.org/debian buster/main armhf libbpp-core-dev armhf 2.4.1-3 [951 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libbpp-seq12 armhf 2.4.1-3 [439 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libbpp-seq-dev armhf 2.4.1-3 [753 kB] -Fetched 29.2 MB in 14s (2085 kB/s) +Fetched 29.2 MB in 4s (8054 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 18932 files and directories currently installed.) @@ -540,7 +574,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libbpp-phyl-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +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 dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-2 dpkg-buildpackage: info: source distribution unstable @@ -582,7 +616,7 @@ -- 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" + cd obj-arm-linux-gnueabihf && make -j6 "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 /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 @@ -591,35 +625,39 @@ make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.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-shared.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-static.dir/DependInfo.cmake --color= -Scanning dependencies of target bpp-phyl-static -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' +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= Scanning dependencies of target bpp-phyl-shared make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build +Scanning dependencies of target bpp-phyl-static +make[3]: Leaving 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' -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++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.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-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.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 -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 +make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build [ 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 -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 [ 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 -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++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp +[ 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++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-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 -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 [ 1%] 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 -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 +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.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 -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 [ 1%] 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 -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 -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.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 -o CMakeFiles/bpp-phyl-static.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-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 -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 +[ 2%] 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 -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 +[ 2%] 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 -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 +[ 2%] 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 -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 In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, @@ -646,16 +684,10 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 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 -o CMakeFiles/bpp-phyl-static.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-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 -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 -[ 2%] 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 -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 -[ 2%] 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 -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 -[ 3%] 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 -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 +[ 3%] 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 -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 +[ 3%] 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 -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++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/../TreeExceptions.h:44, @@ -682,26 +714,24 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 4%] 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 -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 -[ 4%] 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 -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 -[ 4%] 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 -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 -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o +[ 3%] 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 -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 -[ 4%] 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 -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 -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o +[ 3%] 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 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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 -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 -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o +[ 4%] 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 -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 -[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o +[ 4%] 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 -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 +[ 5%] 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 -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 +[ 5%] 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 -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 +[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.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 -o CMakeFiles/bpp-phyl-static.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++/8/vector:69, 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, @@ -714,14 +744,14 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -[ 6%] 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 -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 +[ 5%] 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 -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 +[ 6%] 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 -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 /usr/include/c++/8/bits/vector.tcc: In member function 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -[ 7%] 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 -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 In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -734,8 +764,8 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -[ 7%] 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 -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 +[ 6%] 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 -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 file included from /usr/include/c++/8/vector:64, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -751,109 +781,39 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 7%] 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 -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 -[ 7%] 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 -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 -[ 7%] 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 -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 -[ 8%] 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 -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 -[ 8%] 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 -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 -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o +[ 6%] 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 -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 -In file included from /usr/include/c++/8/vector:69, - 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: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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: -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 8%] 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 -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 -[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o +[ 6%] 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 -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 -[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o +[ 7%] 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=. 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Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o +[ 7%] 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 -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 -[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-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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-I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o +[ 9%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c 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-I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o +[ 9%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c 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-ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 13%] 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 -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 -[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o +[ 10%] 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 -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 +[ 11%] 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 -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 -[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o +[ 11%] 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 -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++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, @@ -868,8 +828,10 @@ vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 -[ 14%] 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 -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 +[ 11%] 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 -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 +[ 11%] 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 -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++/8/vector:64, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -885,26 +847,14 @@ /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ -[ 14%] 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 -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 -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -[ 14%] 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 -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 -/usr/include/c++/8/bits/vector.tcc: In member function 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ +[ 11%] 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 -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 +[ 12%] 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 -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 +[ 12%] 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 -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 +[ 12%] 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 -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++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -939,6 +889,8 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +[ 13%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -999,10 +951,29 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] 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 -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 -[ 15%] 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 -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 +[ 13%] 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 -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++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 13%] 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 -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++/8/algorithm:62, 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, @@ -1060,26 +1031,8 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] 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 -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 -[ 16%] 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 -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 -[ 16%] 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 -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 -[ 16%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ +[ 13%] 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 -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++/8/algorithm:62, 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, @@ -1092,6 +1045,8 @@ __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 13%] 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 -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++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1134,48 +1089,8 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const string&, bool)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 17%] 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 -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 -[ 17%] 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 -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 -In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 17%] 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 -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 -[ 17%] 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 -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 +[ 14%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -1204,6 +1119,8 @@ /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] 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 -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++/8/map:61, from /usr/include/Bpp/Utils/MapTools.h:43, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:46, @@ -1263,45 +1180,14 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] 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 -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 -[ 18%] 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 -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 -[ 18%] 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 -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 -[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o +[ 14%] 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 -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 -In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)': -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o +[ 15%] 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 -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 +[ 15%] 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 -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 +[ 15%] 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 -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 In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1336,10 +1222,41 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 19%] 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 -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 -[ 19%] 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 -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++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)': +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 16%] 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 -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 +[ 16%] 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 -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 +[ 17%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -1397,18 +1314,8 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] 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 -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 -[ 20%] 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 -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 -[ 20%] 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 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp -[ 20%] 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 -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 -[ 20%] 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 -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 -[ 21%] 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 -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 +[ 17%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -1421,8 +1328,8 @@ __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 22%] 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 -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 +[ 17%] 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 -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++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -1465,94 +1372,98 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] 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 -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 -[ 22%] 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 -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 -[ 22%] 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 -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 -[ 22%] 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 -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 -[ 22%] 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 -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 -[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 17%] 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 -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 -[ 23%] 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 -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 -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o +[ 18%] 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 -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 -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o +[ 18%] 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 -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 +[ 18%] 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 -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 -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp -[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o +[ 18%] 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 -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 -[ 25%] Building CXX object 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-I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.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 -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 -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o +[ 19%] 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 -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 -[ 26%] 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 -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 -[ 26%] 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 -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 -[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o +[ 19%] 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 -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 -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o +[ 19%] 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 -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 +[ 20%] 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 -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 -[ 27%] 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 -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 -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o +[ 20%] 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 -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 -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o +[ 20%] 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 -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 -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o +In file included from /usr/include/c++/8/vector:69, + 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: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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: +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 20%] 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 -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 -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o +[ 21%] 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 -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 -[ 29%] 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 -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 -[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o +[ 21%] 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 -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 +[ 21%] 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 -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 -[ 29%] 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 -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 -[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o +[ 21%] 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 -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 file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o +[ 22%] 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 -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 -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)': -/usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - ^ -/usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - ^ +[ 22%] 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 -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++/8/vector:69, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -1565,8 +1476,6 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -[ 30%] 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 -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 In file included from /usr/include/c++/8/vector:64, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -1596,14 +1505,715 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 30%] 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 -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 -[ 30%] 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 -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 -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o +[ 23%] 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 -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 +[ 23%] 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 -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 -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o +[ 23%] 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 -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 +[ 24%] 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 -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 +[ 24%] 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 -o 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-I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 +[ 25%] 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 -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 +[ 25%] 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 -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 +[ 25%] 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 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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 -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 +[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o 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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 -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 +[ 28%] 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 -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 +[ 28%] 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 -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 +[ 28%] 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 -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 +[ 28%] 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 -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 +[ 29%] 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 -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 +[ 29%] 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 -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 +[ 29%] 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 -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 +[ 29%] 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 -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 +[ 30%] 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 -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 +[ 31%] 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 -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 +In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'virtual void bpp::SENCA::setFreq(std::map&)': +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 31%] 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 -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 +[ 31%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 31%] 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 -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 file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 32%] 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 -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 +[ 32%] 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 -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 +[ 32%] 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 -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 +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 32%] 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 -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 +[ 32%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +[ 33%] 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 -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 +[ 33%] 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 -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 file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 33%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +[ 33%] 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 -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 +/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 34%] 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 -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 +[ 34%] 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 -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 +[ 34%] 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 -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 +[ 34%] 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 -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 +[ 35%] 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 -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 +[ 36%] 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 -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 +[ 36%] 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 -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 +[ 36%] 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 -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 +[ 36%] 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 -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 +[ 37%] 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 -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 +[ 37%] 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 -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 +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 37%] 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 -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 file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +[ 37%] 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 -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++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const string&, bool)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 37%] 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 -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 +[ 38%] 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 -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 +[ 38%] 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 -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 +[ 38%] 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 -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 +[ 38%] 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 -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 +[ 39%] 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 -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 +[ 39%] 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 -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 +[ 39%] 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 -o 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-I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 +[ 41%] 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 -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 +[ 41%] 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 -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 +[ 42%] 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 -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 +[ 42%] 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 -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 +In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)': +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 42%] 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 -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 +[ 42%] 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 -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 +[ 43%] 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 -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 +[ 43%] 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 -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 +[ 43%] 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 -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 +[ 43%] 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 -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 +[ 44%] 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 -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 +[ 45%] 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 -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 +[ 45%] 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 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp +[ 45%] 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 -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 +[ 46%] 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 -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 +[ 46%] 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 -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 +[ 46%] 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 -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 +[ 46%] 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 -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 +[ 46%] 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 -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 +[ 46%] 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 -o 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp +[ 48%] 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 -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 +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp +[ 48%] 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 -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 +[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o 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CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp +[ 49%] 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 -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 +[ 49%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp +[ 49%] 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 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp +[ 50%] 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 -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp +[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.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 -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 +[ 50%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp +[ 51%] 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 -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 +[ 51%] 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 -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 +[ 52%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:118:5: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(begin() + (__position - cbegin()), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'void bpp::NNITopologySearch::searchBetter()': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _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:290:87: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + improvement.insert(improvement.begin() + static_cast(pos), diff); + ^ +/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:55: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + improvement.insert(improvement.end(), diff); + ^ +[ 52%] 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 -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 +[ 52%] 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 -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 +[ 52%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp +[ 52%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp +[ 53%] 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 -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 +[ 53%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 53%] 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 -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 +[ 54%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp +[ 54%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp +[ 54%] 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 -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 +[ 54%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp +[ 54%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp +[ 55%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 55%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' {aka '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void 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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 55%] 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 -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 +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + 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++/8/bits/stl_vector.h: In member function 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)': +/usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + ^ +/usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + ^ +[ 55%] 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 -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 +[ 56%] 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 -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 +/usr/include/c++/8/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTools::getBranchLengths(const bpp::Tree&, int)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 56%] 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 -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 +[ 56%] 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 -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 +[ 56%] 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 -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 In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -1638,10 +2248,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 31%] 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 -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 -[ 31%] 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 -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++/8/algorithm:62, 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, @@ -1702,16 +2308,10 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] 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 -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 -[ 32%] 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 -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 -[ 32%] 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 -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 -[ 33%] 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 -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 -[ 33%] 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 -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 +[ 57%] 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 -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 +[ 57%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -1769,20 +2369,32 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] 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 -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 -[ 34%] 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 -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 -[ 34%] 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 -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 -[ 34%] 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 -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 -[ 34%] 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 -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 -[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp -[ 35%] 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 -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 +In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 57%] 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 -o 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std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = const bpp::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 37%] 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 -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 -[ 37%] 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 -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 -[ 37%] 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 -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 -[ 38%] 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 -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 -[ 38%] 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 -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 -[ 38%] 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 -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 -In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'virtual void bpp::SENCA::setFreq(std::map&)': -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 38%] 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 -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 -[ 38%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -1956,6 +2490,8 @@ /usr/include/c++/8/bits/stl_map.h: 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 >]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 59%] 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 -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 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -2002,149 +2538,28 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 38%] 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 -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 -[ 39%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 40%] 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 -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 file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 40%] 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 -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 -[ 40%] 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 -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 file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 40%] 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 -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 -[ 41%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o +[ 59%] 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 -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 -[ 41%] 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 -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 file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)': -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 41%] 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 -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 -[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o +[ 59%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 41%] 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 -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 +[ 60%] 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 -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 +[ 60%] 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 -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 +[ 60%] 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 -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 +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' +[ 60%] Built target bpp-phyl-shared +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= +Scanning dependencies of target test_mapping +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 60%] 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 -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:44, @@ -2179,69 +2594,39 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 42%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -[ 43%] 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 -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++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector >&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -[ 43%] 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 -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 file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:61, + 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++/8/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)': +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +[ 60%] 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 -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 +[ 61%] 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 -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 file included from /usr/include/c++/8/algorithm:62, 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, @@ -2255,15 +2640,6 @@ __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -2294,10 +2670,6 @@ /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, @@ -2312,26 +2684,8 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] 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 -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 -[ 43%] 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 -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 -[ 43%] 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 -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 -[ 44%] 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 -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 -[ 44%] 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 -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 -[ 44%] 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 -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 -[ 44%] 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 -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 -[ 45%] 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 -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 -[ 45%] 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 -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 -[ 45%] 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 -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 +[ 61%] 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 -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 In file included from /usr/include/c++/8/algorithm:62, 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, @@ -2344,8 +2698,8 @@ __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 45%] 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 -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 +[ 61%] 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 -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 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/../Node.h:55, @@ -2389,144 +2743,99 @@ std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': + from /usr/include/Bpp/Io/FileTools.h:46, + from /usr/include/Bpp/App/ApplicationTools.h:44, + from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); +In file included from /usr/include/c++/8/vector:64, + from /usr/include/Bpp/Io/FileTools.h:46, + from /usr/include/Bpp/App/ApplicationTools.h:44, + from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +[ 62%] 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 -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 In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + from /usr/include/Bpp/Io/FileTools.h:46, + from /usr/include/Bpp/App/ApplicationTools.h:44, + from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); +In file included from /usr/include/c++/8/vector:64, + from /usr/include/Bpp/Io/FileTools.h:46, + from /usr/include/Bpp/App/ApplicationTools.h:44, + from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: +/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 45%] 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 -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 -[ 46%] 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 -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 -[ 47%] 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 -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 -[ 47%] 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 -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 -[ 47%] 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 -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 -[ 47%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c 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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 -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 -[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o +[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp -[ 51%] 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 -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 -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o +[ 62%] 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 -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 -[ 51%] 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 -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 -[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o +[ 62%] 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 -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 -[ 51%] 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 -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 -[ 51%] 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 -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 -[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o +[ 62%] 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' +[ 62%] Built target test_mapping +make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.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.dir/DependInfo.cmake --color= +[ 63%] 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 -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 -[ 53%] 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 -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 -[ 53%] 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 -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 -[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o +Scanning dependencies of target test_likelihood +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +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' +[ 63%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.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 -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood.cpp +[ 63%] 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 -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 -[ 53%] 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 -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++/8/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++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - 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++/8/bits/stl_map.h: In member function 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)': -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 54%] 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 -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 -[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o +[ 63%] 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 -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 -[ 54%] 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 -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 -[ 54%] 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 -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 -[ 54%] 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 -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 -[ 55%] 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 -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 -[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o +[ 64%] 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 -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 -[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o +[ 64%] 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 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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 -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 -[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o +[ 65%] 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 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'/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/build +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 65%] Building CXX object test/CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.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 -o CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp +[ 65%] 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 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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 -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 +[ 66%] 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 -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++/8/vector:69, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -2568,154 +2877,102 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 57%] 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 -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 -[ 58%] 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 -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 -[ 59%] 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 -o 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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 -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 -[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o +[ 67%] 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 -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 -[ 60%] 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 -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 -[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o +In file included from /usr/include/c++/8/vector:69, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp:40: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp:40: +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +[ 67%] 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 -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 -[ 61%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c 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/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' +[ 69%] Built target test_likelihood_nh +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= +Scanning dependencies of target test_likelihood_clock +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]: 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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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp -[ 64%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp -[ 64%] Building CXX object 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/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 -o CMakeFiles/bpp-phyl-static.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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) 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/usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'void bpp::NNITopologySearch::searchBetter()': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _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:290:87: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - improvement.insert(improvement.begin() + static_cast(pos), diff); - ^ -/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:55: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - improvement.insert(improvement.end(), diff); - ^ -[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o +[ 72%] 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 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o +[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.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 -o 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 -[ 68%] 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 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-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o +[ 73%] 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' +[ 73%] Built target test_likelihood_clock +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= +Scanning dependencies of target test_simulations +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' +[ 74%] 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 -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_simulations.cpp +[ 74%] 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 -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 -[ 68%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp -[ 68%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o +[ 75%] 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 -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 -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 70%] 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 -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 -[ 70%] 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 -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 +[ 75%] 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 -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 +[ 75%] 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 -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 +[ 76%] 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 -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 +[ 76%] 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 -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++/8/map:60, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:49, @@ -2747,70 +3004,8 @@ __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 70%] 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 -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 -[ 70%] 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 -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 -[ 71%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp -[ 71%] 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 -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 -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 71%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp -[ 71%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp -[ 71%] 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 -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp -[ 72%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ +[ 76%] 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 -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 In file included from /usr/include/c++/8/vector:69, 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, @@ -2829,46 +3024,48 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ +[ 76%] 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 -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 +[ 77%] 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 -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 In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' {aka '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >'} changed in GCC 7.1 + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void 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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); +In file included from /usr/include/c++/8/vector:64, + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: +/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 72%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, - 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++/8/bits/stl_vector.h: In member function 'std::vector bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 72%] 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 -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++/8/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTools::getBranchLengths(const bpp::Tree&, int)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + from /usr/include/Bpp/Numeric/VectorExceptions.h:47, + from /usr/include/Bpp/Numeric/VectorTools.h:43, + from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, + from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: +/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +[ 77%] 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 -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++/8/vector:69, 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, @@ -2887,9 +3084,10 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -[ 73%] 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 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/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 -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 +[ 78%] 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 -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp +[ 79%] 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 -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++/8/vector:69, 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, @@ -2964,6 +3160,10 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ +[ 79%] 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 -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 +[ 79%] 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 -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 file included from /usr/include/c++/8/vector:69, 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, @@ -2982,42 +3182,17 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -[ 75%] 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 -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 -[ 75%] 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 -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 +[ 79%] 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 -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 file included from /usr/include/c++/8/vector:69, - from /usr/include/Bpp/Io/FileTools.h:46, - from /usr/include/Bpp/App/ApplicationTools.h:44, - from /build/libbpp-phyl-2.4.1/test/test_mapping.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/FrequenciesSet/FrequenciesSet.cpp:41: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from /usr/include/Bpp/Io/FileTools.h:46, - from /usr/include/Bpp/App/ApplicationTools.h:44, - from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from /usr/include/Bpp/Io/FileTools.h:46, - from /usr/include/Bpp/App/ApplicationTools.h:44, - from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from /usr/include/Bpp/Io/FileTools.h:46, - from /usr/include/Bpp/App/ApplicationTools.h:44, - from /build/libbpp-phyl-2.4.1/test/test_mapping.cpp:40: -/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45, @@ -3029,15 +3204,6 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45, @@ -3049,14 +3215,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44, @@ -3070,204 +3228,16 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 75%] 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 -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 -[ 75%] 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 -[ 75%] 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 -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 -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 75%] Built target test_mapping -make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.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.dir/DependInfo.cmake --color= -Scanning dependencies of target test_likelihood -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -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' -[ 75%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.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 -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood.cpp -[ 76%] 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 -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 -[ 76%] 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 -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 -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp -[ 76%] Linking CXX executable test_likelihood -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.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.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 -[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 76%] Built target test_likelihood -make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.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_nh.dir/DependInfo.cmake --color= -Scanning dependencies of target test_likelihood_nh -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 76%] Building CXX object test/CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.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 -o CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp -[ 77%] 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 -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 -[ 77%] 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 -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 -[ 77%] 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 -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 -In file included from /usr/include/c++/8/vector:69, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp:40: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_likelihood_nh.cpp:40: -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 78%] 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 -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 file included from /usr/include/c++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 79%] Linking CXX executable test_likelihood_nh -cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_nh.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_nh.dir/test_likelihood_nh.cpp.o -o test_likelihood_nh -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' -[ 79%] Built target test_likelihood_nh -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= -Scanning dependencies of target test_likelihood_clock -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' -[ 80%] 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 -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++/8/vector:69, - 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -[ 80%] 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 -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 -[ 80%] 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 -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 -[ 80%] 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 -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 -[ 80%] 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' -[ 80%] Built target test_likelihood_clock -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= -Scanning dependencies of target test_simulations -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' -[ 81%] 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 -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_simulations.cpp -[ 82%] 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 -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 -[ 82%] 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 -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 -[ 82%] 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 -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++/8/vector:69, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: -/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::NodeTemplate]': +/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from /usr/include/Bpp/Numeric/VectorExceptions.h:47, - from /usr/include/Bpp/Numeric/VectorTools.h:43, - from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43, - from /build/libbpp-phyl-2.4.1/test/test_simulations.cpp:40: -/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -[ 82%] 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 -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 -/usr/include/c++/8/bits/stl_vector.h: In function 'int main()': +/usr/include/c++/8/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 83%] 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 -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 -[ 83%] 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' -[ 83%] Built target test_simulations -make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_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_detailed_simulations.dir/DependInfo.cmake --color= -Scanning dependencies of target test_detailed_simulations -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' -[ 84%] 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 -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp -[ 84%] 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 -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 -[ 84%] 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 -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 +[ 80%] 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 -o 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp +[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp +[ 81%] 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 -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 In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Numeric/VectorExceptions.h:47, from /usr/include/Bpp/Numeric/VectorTools.h:43, @@ -3312,13 +3290,11 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 85%] 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 -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 -[ 85%] Linking CXX executable test_detailed_simulations +[ 81%] 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' -[ 85%] Built target test_detailed_simulations +[ 81%] 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= @@ -3326,12 +3302,56 @@ 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' -[ 85%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o +[ 81%] 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 -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp -[ 85%] 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 -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 -[ 85%] 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 -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 +[ 81%] 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 -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 +[ 81%] 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 -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 +[ 82%] 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 -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 +[ 82%] 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 -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 +[ 82%] 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 -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++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +[ 82%] 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 -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 +[ 83%] 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 -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 +[ 83%] 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 -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 +[ 83%] 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 -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++/8/vector:69, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, @@ -3348,13 +3368,15 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 85%] 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 -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 -[ 86%] Linking CXX executable test_mapping_codon +[ 83%] 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 -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 +[ 84%] 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 -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 +[ 85%] 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' -[ 86%] Built target test_mapping_codon +[ 85%] Built target test_mapping_codon 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= @@ -3362,17 +3384,23 @@ 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' -[ 86%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o +[ 85%] 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 -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_models.cpp -[ 87%] 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 -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 -[ 87%] 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 -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 -[ 87%] Linking CXX executable test_models +[ 85%] 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 -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 +[ 85%] 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 -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 +[ 86%] 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 -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 +[ 86%] 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 -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 +[ 86%] 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 -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 +[ 86%] 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' -[ 87%] Built target test_models +[ 86%] Built target test_models 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= @@ -3380,12 +3408,14 @@ 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' -[ 87%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o +[ 86%] 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 -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_nhx.cpp -[ 87%] 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 -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 -[ 87%] 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 -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 +[ 86%] 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 -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 +[ 87%] 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 -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 +[ 87%] 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 -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 [ 88%] 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 @@ -3400,6 +3430,12 @@ make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' [ 88%] 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 -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_bowker.cpp +[ 88%] 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 -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 +[ 88%] 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 -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 +[ 89%] 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 -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++/8/map:60, from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47, from /usr/include/Bpp/Numeric/Function/Functions.h:45, @@ -3423,8 +3459,12 @@ __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -[ 89%] 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 -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 +[ 89%] 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 -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 +[ 89%] 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 -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 +[ 90%] 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 -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++/8/vector:69, from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45, from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45, @@ -3443,15 +3483,13 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 89%] 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 -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 -[ 89%] Linking CXX executable test_bowker +[ 90%] 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 -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 +[ 90%] 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 -[ 89%] 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 -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 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 89%] Built target test_bowker +[ 90%] Built target test_bowker 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= @@ -3459,13 +3497,17 @@ 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' -[ 89%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o +[ 90%] 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 -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_parsimony.cpp -[ 89%] Linking CXX executable test_parsimony +[ 90%] 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 -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 +[ 90%] 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 -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 +[ 90%] 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 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 89%] Built target test_parsimony +[ 90%] Built target test_parsimony 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= @@ -3473,17 +3515,15 @@ 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' -[ 89%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o +[ 90%] 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 -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree.cpp -[ 90%] 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 -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 -[ 90%] 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 -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 -[ 90%] Linking CXX executable test_tree +[ 91%] 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 -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 +[ 91%] 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' -[ 90%] Built target test_tree +[ 91%] Built target test_tree make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.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_getpath.dir/DependInfo.cmake --color= @@ -3491,13 +3531,13 @@ make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o +[ 92%] 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 -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp -[ 91%] Linking CXX executable test_tree_getpath +[ 92%] Linking CXX executable test_tree_getpath cd /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_getpath.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_getpath.dir/test_tree_getpath.cpp.o -o test_tree_getpath -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' -[ 91%] Built target test_tree_getpath +[ 92%] Built target test_tree_getpath 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= @@ -3505,23 +3545,17 @@ make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o +[ 92%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.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 -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp -[ 92%] Linking CXX executable test_tree_rootat +[ 92%] 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 -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 +[ 92%] 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 -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 +[ 93%] 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 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 92%] Built target test_tree_rootat -[ 92%] 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 -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 -[ 92%] 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 -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 -[ 93%] 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 -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 -[ 93%] 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 -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 -[ 93%] 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 -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 +[ 93%] Built target test_tree_rootat [ 93%] 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 -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 [ 94%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o @@ -3542,6 +3576,10 @@ 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp [ 96%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp +[ 96%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp +[ 97%] 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 -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++/8/vector:69, 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, @@ -3576,10 +3614,6 @@ /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp:296:55: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 improvement.insert(improvement.end(), diff); ^ -[ 96%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp -[ 97%] 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 -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 [ 97%] 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 -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 [ 97%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o @@ -3588,6 +3622,10 @@ 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp [ 98%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp +[ 98%] 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 -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 +[ 98%] 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 -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++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, @@ -3612,14 +3650,16 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 98%] 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 -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 -[ 98%] 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 -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 [ 98%] 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 -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 [ 99%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp +[ 99%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp +[ 99%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp +[100%] 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 -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++/8/vector:69, from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, from /usr/include/Bpp/Seq/SymbolList.h:43, @@ -3644,12 +3684,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -[ 99%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp -[ 99%] 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 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp -[100%] 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 -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++/8/vector:69, from /usr/include/Bpp/Text/TextTools.h:49, from /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.h:44, @@ -3721,43 +3755,43 @@ /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\+=-j3 + cd obj-arm-linux-gnueabihf && make -j6 test ARGS\+=-j6 make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process -j3 +/usr/bin/ctest --force-new-ctest-process -j6 Test project /build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf Start 1: test_bowker Start 2: test_detailed_simulations Start 3: test_likelihood - 1/14 Test #3: test_likelihood .................. Passed 1.33 sec Start 4: test_likelihood_clock - 2/14 Test #4: test_likelihood_clock ............ Passed 1.34 sec Start 5: test_likelihood_nh - 3/14 Test #2: test_detailed_simulations ........ Passed 10.93 sec Start 6: test_mapping - 4/14 Test #6: test_mapping ..................... Passed 17.70 sec + 1/14 Test #4: test_likelihood_clock ............ Passed 0.27 sec Start 7: test_mapping_codon - 5/14 Test #5: test_likelihood_nh ............... Passed 42.26 sec + 2/14 Test #3: test_likelihood .................. Passed 0.49 sec Start 8: test_models - 6/14 Test #8: test_models ...................... Passed 1.04 sec + 3/14 Test #8: test_models ...................... Passed 0.57 sec Start 9: test_nhx - 7/14 Test #9: test_nhx ......................... Passed 0.21 sec + 4/14 Test #9: test_nhx ......................... Passed 0.10 sec Start 10: test_parsimony - 8/14 Test #10: test_parsimony ................... Passed 0.23 sec + 5/14 Test #10: test_parsimony ................... Passed 0.06 sec Start 11: test_simulations - 9/14 Test #1: test_bowker ...................... Passed 183.98 sec + 6/14 Test #2: test_detailed_simulations ........ Passed 5.50 sec Start 12: test_tree -10/14 Test #7: test_mapping_codon ............... Passed 230.11 sec + 7/14 Test #6: test_mapping ..................... Passed 7.75 sec Start 13: test_tree_getpath -11/14 Test #13: test_tree_getpath ................ Passed 0.25 sec + 8/14 Test #13: test_tree_getpath ................ Passed 0.06 sec Start 14: test_tree_rootat -12/14 Test #14: test_tree_rootat ................. Passed 2.23 sec -13/14 Test #12: test_tree ........................ Passed 88.50 sec -14/14 Test #11: test_simulations ................. Passed 420.47 sec + 9/14 Test #14: test_tree_rootat ................. Passed 0.79 sec +10/14 Test #5: test_likelihood_nh ............... Passed 13.89 sec +11/14 Test #12: test_tree ........................ Passed 29.03 sec +12/14 Test #7: test_mapping_codon ............... Passed 78.74 sec +13/14 Test #1: test_bowker ...................... Passed 83.87 sec +14/14 Test #11: test_simulations ................. Passed 154.06 sec 100% tests passed, 0 tests failed out of 14 -Total Test time (real) = 466.98 sec +Total Test time (real) = 155.29 sec make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -3765,7 +3799,7 @@ dh_testroot 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 -j6 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 /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 @@ -3778,49 +3812,31 @@ 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= make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build -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]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +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]: Nothing to be done for 'src/CMakeFiles/bpp-phyl-static.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 46%] Built target bpp-phyl-static make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/CMakeFiles/bpp-phyl-shared.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 46%] Built target bpp-phyl-static [ 92%] Built target bpp-phyl-shared make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/depend make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/depend +make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend +make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend +make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_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_mapping.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/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]: 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_nh.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/build -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_mapping.dir/build.make test/CMakeFiles/test_mapping.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]: Nothing to be done for 'test/CMakeFiles/test_likelihood_nh.dir/build'. -make[3]: Leaving 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood.dir/build'. -make[3]: Leaving 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_mapping.dir/build'. -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 92%] Built target test_mapping -make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend -[ 92%] Built target test_likelihood -[ 93%] Built target test_likelihood_nh -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_likelihood_clock.dir/DependInfo.cmake --color= -make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_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]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' @@ -3828,93 +3844,111 @@ 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]: 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_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/build +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build +make[3]: Leaving 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' make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood_clock.dir/build'. 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_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'test/CMakeFiles/test_detailed_simulations.dir/build'. 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_simulations.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_mapping.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 94%] Built target test_likelihood_clock -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend -[ 95%] Built target test_detailed_simulations -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_mapping_codon.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/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= -[ 96%] Built target test_simulations -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend +make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood_nh.dir/build'. 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]: Nothing to be done for 'test/CMakeFiles/test_detailed_simulations.dir/build'. 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]: 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]: 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_nhx.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_simulations.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' +[ 93%] Built target test_likelihood_clock +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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_models.dir/build'. -make[3]: Leaving 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= +[ 93%] Built target test_likelihood +[ 94%] Built target test_likelihood_nh +make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend +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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_mapping_codon.dir/build'. -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 96%] Built target test_models -[ 97%] Built target test_nhx +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= +[ 94%] Built target test_mapping make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend +[ 95%] Built target test_detailed_simulations +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 -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_bowker.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/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= -[ 98%] Built target test_mapping_codon +[ 96%] Built target test_simulations 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_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build +make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build +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]: 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]: 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 -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' +make[3]: Nothing to be done for 'test/CMakeFiles/test_mapping_codon.dir/build'. 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_bowker.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_models.dir/build'. make[3]: Leaving 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' -make[3]: Nothing to be done for 'test/CMakeFiles/test_tree.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_nhx.dir/build'. +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_tree.dir/build.make test/CMakeFiles/test_tree.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'test/CMakeFiles/test_parsimony.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 98%] Built target test_bowker +[ 96%] Built target test_models +[ 97%] Built target test_mapping_codon make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend -[ 98%] Built target test_parsimony -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' +make[3]: Nothing to be done for 'test/CMakeFiles/test_bowker.dir/build'. +make[3]: Leaving 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' +make[3]: Nothing to be done for 'test/CMakeFiles/test_tree.dir/build'. +make[3]: Leaving 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' 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_getpath.dir/DependInfo.cmake --color= +make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend +[ 98%] Built target test_nhx 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= -[ 98%] Built target test_tree -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build +[ 98%] Built target test_parsimony +[ 98%] Built target test_bowker make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build +[ 98%] Built target test_tree make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'test/CMakeFiles/test_tree_rootat.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_tree_getpath.dir/build'. 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_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'test/CMakeFiles/test_tree_getpath.dir/build'. +make[3]: Nothing to be done for 'test/CMakeFiles/test_tree_rootat.dir/build'. make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-arm-linux-gnueabihf' -[ 99%] Built target test_tree_rootat -[100%] Built target test_tree_getpath +[ 99%] Built target test_tree_getpath +[100%] Built target test_tree_rootat 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 -f CMakeFiles/Makefile2 preinstall @@ -3932,237 +3966,237 @@ -- 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/TreeTools.h --- Installing: /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/TopologySearch.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/Graphics --- 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/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/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/AbstractDendrogramPlot.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/RewardMapping.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/Reward.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/ProbabilisticRewardMapping.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/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/Mapping.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/ProbabilisticSubstitutionMapping.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/Mapping/ProbabilisticRewardMapping.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/SubstitutionMappingTools.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/NaiveSubstitutionCount.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/CategorySubstitutionRegister.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/RewardMapping.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/SubstitutionCount.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/UniformizationSubstitutionCount.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/Mapping/SubstitutionMappingTools.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/Reward.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/NeighborJoining.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/HierarchicalClustering.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/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/DistanceMethod.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/Likelihood --- 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/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/AbstractTreeLikelihoodData.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/TreeLikelihoodTools.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/DRASDRTreeLikelihoodData.h --- 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/TreeLikelihoodData.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/GlobalClockTreeLikelihoodFunctionWrapper.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/DiscreteRatesAcrossSitesTreeLikelihood.h --- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.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/AbstractDiscreteRatesAcrossSitesTreeLikelihood.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/DRTreeLikelihoodTools.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/NNIHomogeneousTreeLikelihood.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/RNonHomogeneousTreeLikelihood.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/RHomogeneousMixedTreeLikelihood.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/HomogeneousTreeLikelihood.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/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/PhyloStatistics.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/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/Parsimony/AbstractTreeParsimonyData.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/DRTreeParsimonyScore.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/BipartitionList.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/TreeTemplateTools.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/MixtureOfSubstitutionModels.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/MixedSubstitutionModel.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/AbstractBiblioMixedSubstitutionModel.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/AbstractWordSubstitutionModel.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/Nucleotide --- 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/RN95.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/T92.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/L95.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/NucleotideSubstitutionModel.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/HKY85.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/gBGC.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/JCnuc.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/SubstitutionModelSetTools.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/GammaDiscreteRateDistribution.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/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/StateMap.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/RegisterRatesSubstitutionModel.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/MixtureOfASubstitutionModel.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/TS98.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/MixtureOfSubstitutionModels.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/WordSubstitutionModel.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/BinarySubstitutionModel.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/FrequenciesSet -- 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/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/WordFrequenciesSet.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/MvaFrequenciesSet.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/RE08.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/FromMixtureSubstitutionModel.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_EX2.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/LLG08_UL3.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/Coala.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/JCprot.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/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/WAG01.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/LLG08_EHO.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/OneChangeTransitionModel.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/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/ConstantRateDistribution.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/GammaDiscreteRateDistribution.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/AbstractBiblioMixedSubstitutionModel.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/AbstractKroneckerWordSubstitutionModel.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/WordSubstitutionModel.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/Codon --- 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/AbstractCodonFrequenciesSubstitutionModel.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/CodonDistancePhaseFrequenciesSubstitutionModel.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_M10.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/AbstractCodonSubstitutionModel.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/CodonAdHocSubstitutionModel.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/AbstractCodonFitnessSubstitutionModel.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/AbstractCodonAAFitnessSubstitutionModel.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/AbstractCodonBGCSubstitutionModel.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/YNGP_M8.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/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/CodonDistanceSubstitutionModel.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/KroneckerCodonDistanceSubstitutionModel.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/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/CodonSubstitutionModel.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/YN98.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/GY94.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/AbstractCodonAAFitnessSubstitutionModel.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/AbstractCodonAARateSubstitutionModel.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/YNGP_M.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/AbstractKroneckerCodonSubstitutionModel.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/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/CodonDistanceFrequenciesSubstitutionModel.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/AbstractMixedSubstitutionModel.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/Protein --- 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/DSO78.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/LG10_EX_EHO.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/LLG08_UL3.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/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/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/WAG01.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/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/LGL08_CAT.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/KroneckerWordSubstitutionModel.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/AbstractCodonDistanceSubstitutionModel.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/YNGP_M2.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/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/KroneckerCodonDistanceFrequenciesSubstitutionModel.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/AbstractBiblioSubstitutionModel.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/AbstractFromSubstitutionModelTransitionModel.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/G2001.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/Nucleotide +-- 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/HKY85.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/TN93.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/K80.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/NucleotideSubstitutionModel.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/T92.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/RN95s.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/F84.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/FromMixtureSubstitutionModel.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/MixedSubstitutionModel.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/G2001.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/TreeExceptions.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/OptimizationTools.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/PhyloStatistics.h +-- Installing: /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/AncestralStateReconstruction.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/DRTreeParsimonyData.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/DRTreeParsimonyScore.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/SitePatterns.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/NodeTemplate.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/DetailedSiteSimulator.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/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/SiteSimulator.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/SequenceSimulationTools.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/Io --- 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/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/IoFrequenciesSetFactory.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/BppOFrequenciesSetFormat.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/IoDistanceMatrixFactory.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/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/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/IoFrequenciesSetFactory.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/BppOTreeWriterFormat.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/BppOTreeReaderFormat.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/IoFrequenciesSet.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/IoSubstitutionModelFactory.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/IoDistanceMatrixFactory.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/IoSubstitutionModel.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/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/IoDistanceMatrix.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/Simulation --- 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/SequenceSimulationTools.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/MutationProcess.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/NodeTemplate.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/TreeTemplate.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/BppOMultiTreeWriterFormat.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/BppOTreeWriterFormat.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/TreeTools.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/AbstractTreeLikelihoodData.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/NonHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.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/AbstractNonHomogeneousTreeLikelihood.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/TreeLikelihoodData.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/DRNonHomogeneousTreeLikelihood.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/PairedSiteLikelihoods.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/MarginalAncestralStateReconstruction.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.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/RHomogeneousTreeLikelihood.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/TreeLikelihood.h +-- Installing: /build/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.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/PseudoNewtonOptimizer.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/ClockTreeLikelihood.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/AbstractHomogeneousTreeLikelihood.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/RNonHomogeneousMixedTreeLikelihood.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/BipartitionList.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/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/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/TopologySearch.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/PatternTools.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/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/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/NeighborJoining.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/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' @@ -4209,21 +4243,23 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-2_armhf.deb'. dpkg-deb: building package 'libbpp-phyl12' in '../libbpp-phyl12_2.4.1-2_armhf.deb'. dpkg-deb: building package 'libbpp-phyl12-dbgsym' in '../libbpp-phyl12-dbgsym_2.4.1-2_armhf.deb'. -dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libbpp-phyl_2.4.1-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/21847/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21847/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/13564 and its subdirectories -I: Current time: Mon Jun 8 13:58:39 -12 2020 -I: pbuilder-time-stamp: 1591667919 +I: removing directory /srv/workspace/pbuilder/21847 and its subdirectories +I: Current time: Tue Jun 9 16:37:29 +14 2020 +I: pbuilder-time-stamp: 1591670249