I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 29 07:58:07 +14 2020 I: pbuilder-time-stamp: 1593367087 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libmems_1.6.0+4725-8.dsc] I: copying [./libmems_1.6.0+4725.orig.tar.xz] I: copying [./libmems_1.6.0+4725-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Aug 28 09:51:46 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libmems_1.6.0+4725-8.dsc dpkg-source: info: extracting libmems in libmems-1.6.0+4725 dpkg-source: info: unpacking libmems_1.6.0+4725.orig.tar.xz dpkg-source: info: unpacking libmems_1.6.0+4725-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_fix_ctors.patch dpkg-source: info: applying 02_fix_a_Wformat.patch dpkg-source: info: applying pkg-config-directive.patch dpkg-source: info: applying 03_update_boost_m4_to_git_d9ff75.patch dpkg-source: info: applying 04_add_dependend_libs_to_link_command.patch dpkg-source: info: applying 05_gcc-6.patch dpkg-source: info: applying boost1.62.patch dpkg-source: info: applying drop-version-number.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/12796/tmp/hooks/D01_modify_environment starting debug: Running on odu3a. 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/12796/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/12796/tmp/hooks/D02_print_environment starting I: set 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=4' 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=7f9d5d74e6974ac5ad498a2f19b39870 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=12796 PS4='+ ' 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.b4g6CGblIS/pbuilderrc_UjJk --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.b4g6CGblIS/b2 --logfile b2/build.log libmems_1.6.0+4725-8.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 i-capture-the-hostname 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 -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 29 07:58 sh -> bash lrwxrwxrwx 1 root root 4 Jun 28 22:27 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/12796/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libgenome-dev; however: Package libgenome-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-filesystem-dev{a} libboost-filesystem1.67-dev{a} libboost-filesystem1.67.0{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-system1.67-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgenome-dev{a} libgenome0{a} libglib2.0-0{a} libicu-dev{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libmuscle-dev{a} libmuscle1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After unpacking 259 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf d-shlibs all 0.84 [17.2 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 25 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main armhf icu-devtools armhf 63.1-6+deb10u1 [168 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libboost-filesystem1.67.0 armhf 1.67.0-13+deb10u1 [255 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libboost-system1.67-dev armhf 1.67.0-13+deb10u1 [232 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libboost-filesystem1.67-dev armhf 1.67.0-13+deb10u1 [262 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libboost-filesystem-dev armhf 1.67.0.1 [3684 B] Get: 41 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libicu-dev armhf 63.1-6+deb10u1 [8940 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libboost-regex1.67-dev armhf 1.67.0-13+deb10u1 [538 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13+deb10u1 [254 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libboost-iostreams-dev armhf 1.67.0.1 [3632 B] Get: 46 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67.0 armhf 1.67.0-13+deb10u1 [336 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67-dev armhf 1.67.0-13+deb10u1 [385 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libboost-program-options-dev armhf 1.67.0.1 [3656 B] Get: 49 http://deb.debian.org/debian buster/main armhf libgenome0 armhf 1.3.11+svn20110227.4616-2 [98.1 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libgenome-dev armhf 1.3.11+svn20110227.4616-2 [174 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libmuscle1 armhf 3.7+4565-6 [202 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libmuscle-dev armhf 3.7+4565-6 [256 kB] Get: 53 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Fetched 39.2 MB in 6s (6543 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.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. 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Setting up libboost1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libboost-program-options1.67.0:armhf (1.67.0-13+deb10u1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libgenome0:armhf (1.3.11+svn20110227.4616-2) ... Setting up libmuscle1 (3.7+4565-6) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libgenome-dev (1.3.11+svn20110227.4616-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libboost-program-options1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:armhf (1.67.0.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... 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Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libboost-filesystem-dev:armhf (1.67.0.1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libboost-iostreams-dev:armhf (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/libmems-1.6.0+4725/ && 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 libmems dpkg-buildpackage: info: source version 1.6.0+4725-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:54: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.ac:66: installing 'config/compile' configure.ac:66: installing 'config/config.guess' configure.ac:66: installing 'config/config.sub' configure.ac:54: installing 'config/install-sh' configure.ac:54: installing 'config/missing' libMems/Makefile.am:48: warning: source file 'HomologyHMM/algebras.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. libMems/Makefile.am:48: warning: source file 'HomologyHMM/homology.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:48: warning: source file 'HomologyHMM/homologymain.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/asyncio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alinuxaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/aPOSIXaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alibc.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/awin32aio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/buffer.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/util.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sorting.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/dmsort.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/timing.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sml.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am: installing 'config/depcomp' dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking whether ln -s works... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for ANSI C header files... (cached) yes checking for Boost headers version >= 1.34.0... yes checking for Boost's header version... 1_67 checking whether the compiler implements namespaces... yes checking for the toolset name used by Boost for g++... configure: WARNING: could not figure out which toolset name to use for g++ checking boost/system/error_code.hpp usability... yes checking boost/system/error_code.hpp presence... yes checking for boost/system/error_code.hpp... yes checking for the Boost system library... yes checking boost/filesystem/path.hpp usability... yes checking boost/filesystem/path.hpp presence... yes checking for boost/filesystem/path.hpp... yes checking for the Boost filesystem library... (cached) yes checking boost/program_options.hpp usability... yes checking boost/program_options.hpp presence... yes checking for boost/program_options.hpp... yes checking for the Boost program_options library... (cached) yes checking boost/iostreams/device/file_descriptor.hpp usability... yes checking boost/iostreams/device/file_descriptor.hpp presence... yes checking for boost/iostreams/device/file_descriptor.hpp... yes checking for the Boost iostreams library... (cached) yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for sys/types.h... (cached) yes checking sys/aio.h usability... no checking sys/aio.h presence... no checking for sys/aio.h... no checking aio.h usability... yes checking aio.h presence... yes checking for aio.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking for pthread_mutex_unlock in -lpthread... yes checking for aio_write in -lrt... yes checking for doxygen... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for perl... /usr/bin/perl checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking whether gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libMems/Makefile config.status: creating libMems.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j4 make[1]: Entering directory '/build/libmems-1.6.0+4725' make all-recursive make[2]: Entering directory '/build/libmems-1.6.0+4725' Making all in libMems make[3]: Entering directory '/build/libmems-1.6.0+4725/libMems' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /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 mems::bmer&}; _Tp = mems::bmer; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual boolean mems::MemorySML::Read(std::vector&, gnSeqI, gnSeqI)': /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/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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_algo.h: In member function 'virtual void mems::MemorySML::Create(const genome::gnSequence&, uint64)': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /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 long long unsigned int&}; _Tp = long long unsigned int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const': /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); ^~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp MatchFinder.cpp:126:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ MatchFinder.cpp:126:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /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 long long int&}; _Tp = long long int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /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 = {long long unsigned int}; _Tp = long long unsigned int; _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 = {long long unsigned int}; _Tp = long long unsigned int; _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)...); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /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 long long unsigned int&}; _Tp = long long unsigned int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FindAll(const string&, 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); ^~~~~~~~~~~~~~~~~ SortedMerList.cpp:229:1: 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqI, 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); ^~~~~~~~~~~~~~~~~ SortedMerList.cpp:579:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /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 mems::bmer&}; _Tp = mems::bmer; _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:413:7: 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, 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: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 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, 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: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); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /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 long long int&}; _Tp = long long int; _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>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _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 In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::FileSML::RadixSort(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: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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /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 = {long long int}; _Tp = long long int; _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 = {long long int}; _Tp = long long int; _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)...); ^~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::FileSML::LoadFile(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/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)': /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/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp: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); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ /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/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'virtual void mems::FileSML::Create(const genome::gnSequence&, uint64)': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/UngappedLocalAlignment.h:18, from ../libMems/Match.h:19, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: /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 long long int&}; _Tp = long long int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/UngappedLocalAlignment.h:18, from ../libMems/Match.h:19, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 } ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /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 long long int&}; _Tp = long long int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /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 = {long long unsigned int}; _Tp = long long unsigned int; _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 'virtual void mems::MemHash::FindMatches(mems::MatchList&)': /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)...); ^~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 In file included from /usr/include/c++/8/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Aligner.cpp:10: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/include/c++/8/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Islands.cpp:13: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /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 long long int&}; _Tp = long long int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /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 mems::Island&}; _Tp = mems::Island; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::simpleFindIslands(mems::IntervalList&, uint, 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); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _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>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _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 In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/Interval.h:21, from ../libMems/IntervalList.h:22, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /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 mems::GappedAlignment&}; _Tp = mems::GappedAlignment; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /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 long long int&}; _Tp = long long int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::simpleFindBackbone(mems::IntervalList&, uint, uint, 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: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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::CreateGapSearchList(std::vector&, const std::vector&, std::vector > >&, boolean)': /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); ^~~~~~~~~~~~~~~~~ /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 long long unsigned int&}; _Tp = long long unsigned int; _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/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/GappedAligner.h:18, from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/HybridAbstractMatch.h:202:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /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 long long unsigned int&}; _Tp = long long unsigned int; _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/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/Interval.h:18, from ../libMems/IntervalList.h:22, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /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 = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void mems::addUnalignedIntervals(mems::IntervalList&, std::set, std::vector)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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); ^~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/GappedAlignment.h:18, from GappedAlignment.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: 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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /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 = {long long unsigned int}; _Tp = long long unsigned int; _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:413:7: 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /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 ../libMems/GappedAlignment.h:18, from GappedAlignment.cpp:13: ../libMems/SparseAbstractMatch.h:144:1: 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/SparseAbstractMatch.h:195:1: 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /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 mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In function 'int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)': /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 ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /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 long long int&}; _Tp = long long int; _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>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _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>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _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 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: 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 ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /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 = {long long unsigned int}; _Tp = long long unsigned int; _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:413:7: 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:64, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /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 ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: ../libMems/SparseAbstractMatch.h:144:1: 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, 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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MuscleInterface.cpp:519:1: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 } ^ /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::computeLCBAdjacencies_v2(mems::IntervalList&, std::vector >&, std::vector&)': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, 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:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v2(std::vector >*> >&, std::vector >&, std::vector&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ MuscleInterface.cpp:672:1: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 } ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >*> >&, boolean, std::ostream*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: /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 long long int&}; _Tp = long long int; _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/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/RepeatMatchList.h:20, from RepeatMatchList.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /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 long long int&}; _Tp = long long int; _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 ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/MatchHashEntry.h:19, from ../libMems/RepeatMatch.h:20, from RepeatMatch.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 } ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o In file included from /usr/include/c++/8/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o In file included from /usr/include/c++/8/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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 mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: ../libMems/SparseAbstractMatch.h:195:1: 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:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /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 = {long long int}; _Tp = long long int; _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 mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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)...); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /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 long long unsigned int&}; _Tp = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 long long unsigned int&}; _Tp = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 mems::SuperInterval&}; _Tp = mems::SuperInterval; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::applyBreakpoints(std::vector&, std::vector&, Maniplator&) [with T = mems::SuperInterval; Maniplator = mems::SuperIntervalManipulator]': /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 long long int&}; _Tp = long long int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]': /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /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 ../libMems/Match.h:22, from ../libMems/Interval.h:21, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: 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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::push_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = mems::MoveScoreHeapComparator]': /usr/include/c++/8/bits/stl_heap.h:189:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 push_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:189:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /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 mems::LCB&}; _Tp = mems::LCB; _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:413:7: 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/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from GreedyBreakpointElimination.cpp:7: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::chooseNextAlignmentPair(PhyloTree&, node_id_t&, node_id_t&, node_id_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); ^~~~~~~~~~~~~~~~~ /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: 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:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: 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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 mems::LCB&}; _Tp = mems::LCB; _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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_equal_to_iter]': /usr/include/c++/8/bits/stl_algo.h:962:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unique(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:962:5: 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:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /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 long long unsigned int&}; _Tp = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: 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: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _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*, std::vector > >'} 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}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' 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>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _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 = {long long unsigned int}; _Tp = long long unsigned int; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /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:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /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 mems::LCB&}; _Tp = mems::LCB; _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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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:63, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator*>*, std::vector*> > >; _ForwardIterator = mems::TrackingLCB*>*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*>*, std::vector*> > >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*>*, std::vector*> > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = mems::TrackingLCB*>; _Alloc = std::allocator*> >]': /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*>*, std::vector*> > >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In constructor 'mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array, boost::multi_array, std::vector*>, mems::PairwiseLCBMatrix&, std::vector&, std::vector&, boost::multi_array&, boost::multi_array&, size_t, size_t, size_t, size_t)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /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 mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_heap.h: In function 'double mems::greedySearch(SearchScorer&) [with SearchScorer = mems::EvenFasterSumOfPairsBreakpointScorer]': /usr/include/c++/8/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__make_heap(__first, __last, __cmp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../libMems/Aligner.h:26, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/GreedyBreakpointElimination.h:845:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::push_heap( move_heap.begin(), move_heap.begin()+heap_end+newdI+1, mshc ); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from ../libMems/Aligner.h:26, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/GreedyBreakpointElimination.h:729:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::push_heap( move_heap.begin(), move_heap.begin()+prev_size+newdI+1, mshc ); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__make_heap(__first, __last, __cmp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::GreedyRemovalScorer]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from ../libMems/Aligner.h:26, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/GreedyBreakpointElimination.h:729:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::push_heap( move_heap.begin(), move_heap.begin()+prev_size+newdI+1, mshc ); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__make_heap(__first, __last, __cmp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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 mems::AlignmentTreeNode&}; _Tp = mems::AlignmentTreeNode; _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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator]': /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); ^~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __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 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o In file included from /usr/include/c++/8/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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:69, from /usr/include/c++/8/backward/hashtable.h:62, from /usr/include/c++/8/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'node_id_t mems::createAlignmentTreeRoot(PhyloTree&, node_id_t, node_id_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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/c++/8/backward/hashtable.h:62, from /usr/include/c++/8/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/8/bits/stl_vector.h: In member function 'void SimplePath::addEdge(int, double, std::vector&, int, 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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector >*, std::allocator >*> >]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector*>]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o In file included from /usr/include/c++/8/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homologymain.cc:21: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o /usr/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree::readTree(std::istream&) [with T = mems::AlignmentTreeNode]': /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); ^~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO': dmSML/aPOSIXaio.c:115:21: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types] rval = aio_suspend(request_array, 1, &zero_wait); ^~~~~~~~~~~~~ In file included from /usr/include/features.h:424, from /usr/include/arm-linux-gnueabihf/sys/types.h:25, from ../libMems/dmSML/asyncio.h:24, from ../libMems/dmSML/aPOSIXaio.h:8, from dmSML/aPOSIXaio.c:5: /usr/include/aio.h:198:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' extern int __REDIRECT_NTH (aio_suspend, ^~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o dmSML/util.c: In function 'removeFile': dmSML/util.c:126:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] rm_cmd = Fmt( "/bin/rm -fv %s", filename ); ^ dmSML/util.c:128:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] rm_cmd = Fmt( "/bin/rm -f %s", filename ); ^ dmSML/util.c:129:16: warning: implicit declaration of function 'system' [-Wimplicit-function-declaration] return system( rm_cmd ); ^~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /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 __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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericIntervalList<>]': /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 function 'void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericMatchList >*>]': /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 ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::unalignIslands(mems::IntervalList&, std::vector*>&, std::vector >*, std::allocator >*> > >&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' 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 ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]': /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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /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 ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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_algo.h: In function 'void mems::applyAncestralBreakpoints(const std::vector&, std::vector&, uint, Manipulator&) [with T = mems::SuperInterval; Manipulator = mems::SuperIntervalManipulator]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::applyAncestralBreakpoints(const std::vector&, std::vector&, uint, Manipulator&) [with T = mems::AbstractMatch*; Manipulator = mems::GenericMatchSeqManipulator<>]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1004:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__unique(__first, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_equal_to_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp: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)); ^ /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = 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/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1004:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__unique(__first, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_equal_to_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp: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)); ^ /usr/include/c++/8/bits/stl_vector.h: In function 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = mems::GenericMatchList >*>]': /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 mems::ProgressiveAligner::pairwiseAnchorSearch(mems::MatchList&, mems::Match*, mems::Match*, const mems::AbstractMatch*, uint, uint)': /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); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 In file included from /usr/include/c++/8/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/stl_algo.h: In member function 'void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)': /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void mems::ProgressiveAligner::getAlignment(mems::IntervalList&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/arm-linux-gnueabihf RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/8/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/arm-linux-gnueabihf/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/8/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems.so.1 -o .libs/libMems.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libMems.so.1" && ln -s "libMems.so.1.0.0" "libMems.so.1") libtool: link: (cd ".libs" && rm -f "libMems.so" && ln -s "libMems.so.1.0.0" "libMems.so") libtool: link: ar cru .libs/libMems.a RepeatHash.o DNAFileSML.o MatchFinder.o DNAMemorySML.o MemorySML.o SortedMerList.o FileSML.o MemHash.o MatchHashEntry.o Interval.o IntervalList.o twister.o gnAlignedSequences.o MatchList.o Aligner.o Islands.o MaskedMemHash.o GappedAlignment.o MuscleInterface.o PhyloTree.o RepeatMatchList.o RepeatMatch.o Backbone.o PairwiseMatchFinder.o ProgressiveAligner.o SuperInterval.o GreedyBreakpointElimination.o algebras.o homology.o homologymain.o asyncio.o alinuxaio.o aPOSIXaio.o alibc.o awin32aio.o buffer.o util.o sorting.o dmsort.o timing.o sml.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libMems.a libtool: link: ( cd ".libs" && rm -f "libMems.la" && ln -s "../libMems.la" "libMems.la" ) make[3]: Leaving directory '/build/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/build/libmems-1.6.0+4725' make[3]: Leaving directory '/build/libmems-1.6.0+4725' make[2]: Leaving directory '/build/libmems-1.6.0+4725' make[1]: Leaving directory '/build/libmems-1.6.0+4725' dh_auto_test make -j4 check VERBOSE=1 make[1]: Entering directory '/build/libmems-1.6.0+4725' Making check in libMems make[2]: Entering directory '/build/libmems-1.6.0+4725/libMems' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/build/libmems-1.6.0+4725' make[2]: Leaving directory '/build/libmems-1.6.0+4725' make[1]: Leaving directory '/build/libmems-1.6.0+4725' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libmems-1.6.0+4725' Making install in libMems make[2]: Entering directory '/build/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/build/libmems-1.6.0+4725/libMems' /bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/sh ../libtool --mode=install /usr/bin/install -c libMems.la '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 libtool: install: (cd /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libMems.so.1.0.0 libMems.so.1 || { rm -f libMems.so.1 && ln -s libMems.so.1.0.0 libMems.so.1; }; }) libtool: install: (cd /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; }) libtool: install: /usr/bin/install -c .libs/libMems.lai /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.la libtool: install: /usr/bin/install -c .libs/libMems.a /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: install: chmod 644 /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: install: ranlib /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/dmSML' /usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/dmSML' /bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/HomologyHMM' /usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/HomologyHMM' /bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems' /usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems' /usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems' make[3]: Leaving directory '/build/libmems-1.6.0+4725/libMems' make[2]: Leaving directory '/build/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/build/libmems-1.6.0+4725' make[3]: Entering directory '/build/libmems-1.6.0+4725' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 libMems.pc '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[3]: Leaving directory '/build/libmems-1.6.0+4725' make[2]: Leaving directory '/build/libmems-1.6.0+4725' make[1]: Leaving directory '/build/libmems-1.6.0+4725' debian/rules override_dh_install make[1]: Entering directory '/build/libmems-1.6.0+4725' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libGenome0-dev/libgenome-dev/ \ --override s/libMUSCLE1-dev/libmuscle-dev/ \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libboost-filesystem1.67-dev package exists. --> libboost-iostreams1.67-dev package exists. --> libboost-system1.67-dev package exists. --> libgenome-dev package exists. --> libmuscle-dev package exists. set -e install -d -m 755 debian/libmems-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libmems1/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a debian/libmems-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so debian/libmems-dev/usr/lib/arm-linux-gnueabihf mv /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1 debian/libmems1/usr/lib/arm-linux-gnueabihf mv /build/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 debian/libmems1/usr/lib/arm-linux-gnueabihf PKGDEV=libmems-dev PKGSHL=libmems1 install -d -m 755 debian/libmems-dev/usr mv debian/tmp/usr/include debian/libmems-dev/usr install -d -m 755 debian/libmems-dev/usr/lib/arm-linux-gnueabihf/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-dev/usr/lib/arm-linux-gnueabihf/pkgconfig make[1]: Leaving directory '/build/libmems-1.6.0+4725' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libmems1/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libmems1/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 was not linked against libboost_system.so.1.67.0 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libmems1' in '../libmems1_1.6.0+4725-8_armhf.deb'. dpkg-deb: building package 'libmems-dev' in '../libmems-dev_1.6.0+4725-8_armhf.deb'. dpkg-deb: building package 'libmems1-dbgsym' in '../libmems1-dbgsym_1.6.0+4725-8_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libmems_1.6.0+4725-8_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/12796/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/12796/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/12796 and its subdirectories I: Current time: Mon Jun 29 08:26:49 +14 2020 I: pbuilder-time-stamp: 1593368809