I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 23 03:12:13 +14 2021 I: pbuilder-time-stamp: 1629637933 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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+4725-9.dsc] I: copying [./libmems_1.6.0+4725.orig.tar.xz] I: copying [./libmems_1.6.0+4725-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.9J6hYnTZ/trustedkeys.kbx': General error gpgv: Signature made Tue Nov 17 23:02:37 2020 +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+4725-9.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+4725-9.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3782/tmp/hooks/D01_modify_environment starting debug: Running on virt64a. 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/3782/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3782/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]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(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,-fixfilepath 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=a041240f482546a4a82e2fec34cb60dd 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=3782 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.kKzjAhCsuZ/pbuilderrc_ufaW --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.kKzjAhCsuZ/b2 --logfile b2/build.log libmems_1.6.0+4725-9.dsc' SUDO_GID=114 SUDO_UID=108 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 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 23 03:13 sh -> bash lrwxrwxrwx 1 root root 4 Aug 21 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/3782/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-compat (= 13), 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 ... 19398 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-compat (= 13); however: Package debhelper-compat 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} bsdextrautils{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-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgenome-dev{a} libgenome0{a} libglib2.0-0{a} libicu-dev{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{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 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 41.9 MB of archives. After unpacking 276 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf d-shlibs all 0.98 [17.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf icu-devtools armhf 67.1-7 [180 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libboost-filesystem1.74.0 armhf 1.74.0-9 [275 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libboost-system1.74.0 armhf 1.74.0-9 [242 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libboost-system1.74-dev armhf 1.74.0-9 [243 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libboost-filesystem1.74-dev armhf 1.74.0-9 [289 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libboost-filesystem-dev armhf 1.74.0.3 [4368 B] Get: 40 http://deb.debian.org/debian bullseye/main armhf libboost-regex1.74.0 armhf 1.74.0-9 [459 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libicu-dev armhf 67.1-7 [9343 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libboost-regex1.74-dev armhf 1.74.0-9 [572 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libboost-iostreams1.74-dev armhf 1.74.0-9 [271 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libboost-iostreams-dev armhf 1.74.0.3 [4316 B] Get: 45 http://deb.debian.org/debian bullseye/main armhf libboost-program-options1.74.0 armhf 1.74.0-9 [339 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libboost-program-options1.74-dev armhf 1.74.0-9 [384 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libboost-program-options-dev armhf 1.74.0.3 [4340 B] Get: 48 http://deb.debian.org/debian bullseye/main armhf libgenome0 armhf 1.3.11+svn20110227.4616-3 [102 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libgenome-dev armhf 1.3.11+svn20110227.4616-3 [180 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libmuscle1 armhf 3.7+4565-7 [201 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libmuscle-dev armhf 3.7+4565-7 [259 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Fetched 41.9 MB in 6s (7104 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libmems_1.6.0+4725-9_source.changes dpkg-buildpackage: info: source package libmems dpkg-buildpackage: info: source version 1.6.0+4725-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary 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-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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_74 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 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual boolean mems::MemorySML::Read(std::vector&, gnSeqI, gnSeqI)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from MemorySML.cpp:14: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In member function 'virtual void mems::MemorySML::Create(const genome::gnSequence&, uint64)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | 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 -fdebug-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 /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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MatchFinder.cpp:126:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 126 | } | ^ MatchFinder.cpp:126:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'virtual void mems::MatchFinder::FindMatchSeeds(const std::vector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'virtual void mems::MatchFinder::FindMatchSeeds()': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ /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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FindAll(const string&, std::vector)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ SortedMerList.cpp:229:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 229 | } | ^ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqI, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ SortedMerList.cpp:579:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 579 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::FileSML::RadixSort(std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void mems::FileSML::LoadFile(const string&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector&, int)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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 -fdebug-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 -fdebug-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++/10/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++/10/bits/stl_algo.h: In member function 'virtual void mems::FileSML::Create(const genome::gnSequence&, uint64)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | 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 -fdebug-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 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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ 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 -fdebug-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 /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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'virtual void mems::MemHash::FindMatches(mems::MatchList&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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 -fdebug-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 /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 -fdebug-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 -fdebug-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: 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/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++/10/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] 32 | #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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.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 -fdebug-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 In file included from /usr/include/c++/10/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++/10/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] 32 | #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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 223 | __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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::simpleFindIslands(mems::IntervalList&, uint, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:144:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function 'void mems::addUnalignedIntervals(mems::IntervalList&, std::set, std::vector)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::simpleFindBackbone(mems::IntervalList&, uint, uint, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::CreateGapSearchList(std::vector&, const std::vector&, std::vector > >&, boolean)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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' changed in GCC 7.1 144 | } | ^ /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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o /usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function 'void mems::ComputeLCBs(mems::MatchList&, std::set&, std::vector >*> >&, std::vector >&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:144:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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 -fdebug-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++/10/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++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/vector.tcc: In member function 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp MuscleInterface.cpp:519:1: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 519 | } | ^ MuscleInterface.cpp:519:1: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 MuscleInterface.cpp:519:1: note: parameter passing for argument of type 'std::vector >::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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/vector.tcc: In member function 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MuscleInterface.cpp:672:1: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 672 | } | ^ MuscleInterface.cpp:672:1: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 MuscleInterface.cpp:672:1: note: parameter passing for argument of type 'std::vector >::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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void mems::computeLCBAdjacencies_v2(mems::IntervalList&, std::vector >&, std::vector&)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v2(std::vector >*> >&, std::vector >&, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::filterMatches(std::vector&, std::vector >*> >&, std::vector >&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >*> >&, boolean, std::ostream*)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ /usr/include/c++/10/bits/stl_vector.h: In member function 'void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::string)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1198 | _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 -fdebug-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 /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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ 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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.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 -fdebug-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++/10/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++/10/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] 32 | #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 -fdebug-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 -fdebug-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.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 -fdebug-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 In file included from /usr/include/c++/10/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++/10/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] 32 | #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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: ../libMems/SparseAbstractMatch.h:144:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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 -fdebug-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 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __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 -fdebug-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 -fdebug-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++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/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] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 939 | __unique(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function 'void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector >*, std::allocator >*> >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector*>]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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' changed in GCC 7.1 195 | } | ^ /usr/include/c++/10/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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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:144:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In 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++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc:721:7: 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++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __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 -fdebug-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 -fdebug-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++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::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 -fdebug-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 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 -fdebug-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++/10/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/10/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] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 ProgressiveAligner.cpp:14: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 202 | } | ^ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/backward/hashtable.h:62, from /usr/include/c++/10/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/backward/hashtable.h:62, from /usr/include/c++/10/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/10/bits/stl_vector.h: In member function 'void SimplePath::addEdge(int, double, std::vector&, int, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { 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 ProgressiveAligner.cpp:14: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 195 | } | ^ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:339:5: 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++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 1665 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1666 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1665:19: 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++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/bits/stl_heap.h:412:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 412 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:412:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function 'double mems::greedySearch(SearchScorer&) [with SearchScorer = mems::EvenFasterSumOfPairsBreakpointScorer]': /usr/include/c++/10/bits/stl_heap.h:412:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 412 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::chooseNextAlignmentPair(PhyloTree&, node_id_t&, node_id_t&, node_id_t&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::makeAllPairwiseGenomeHSS(mems::IntervalList&, std::vector*>&, std::vector*>&, mems::pairwise_genome_hss_t&, const mems::HssDetector*)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/vector.tcc: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1431 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: ../libMems/SparseAbstractMatch.h:144:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 144 | } | ^ In file included from /usr/include/c++/10/vector:67, 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++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /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 -fdebug-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 -fdebug-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++/10/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homologymain.cc:21: /usr/include/c++/10/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] 32 | #warning \ | ^~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::unalignIslands(mems::IntervalList&, std::vector*>&, std::vector >*, std::allocator >*> > >&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'node_id_t mems::createAlignmentTreeRoot(PhyloTree&, node_id_t, node_id_t)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/include/c++/10/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++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __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 -fdebug-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 In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In member function 'void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_t)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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 -fdebug-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 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 -fdebug-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 -fdebug-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 -fdebug-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] 115 | rval = aio_suspend(request_array, 1, &zero_wait); | ^~~~~~~~~~~~~ | | | struct aiocb ** In file included from /usr/include/features.h:461, 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 **' 198 | 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 -fdebug-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 /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 -fdebug-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 -fdebug-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 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 -fdebug-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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h: In member function 'void PhyloTree::readTree(std::istream&) [with T = mems::AlignmentTreeNode]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1198 | _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 -fdebug-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 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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] 126 | rm_cmd = Fmt( "/bin/rm -fv %s", filename ); | ^ dmSML/util.c:128:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 128 | rm_cmd = Fmt( "/bin/rm -f %s", filename ); | ^ dmSML/util.c:129:16: warning: implicit declaration of function 'system' [-Wimplicit-function-declaration] 129 | 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 -fdebug-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 /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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /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 -fdebug-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 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 -fdebug-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 /usr/include/c++/10/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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericIntervalList<>]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericMatchList >*>]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 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 -fdebug-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 /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 -fdebug-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 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In member function 'void mems::ProgressiveAligner::propagateDescendantBreakpoints(node_id_t, uint, std::vector&) [with MatchType = mems::AbstractMatch]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 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 -fdebug-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 /usr/include/c++/10/bits/vector.tcc: In member function 'void mems::ProgressiveAligner::propagateDescendantBreakpoints(node_id_t, uint, std::vector&) [with MatchType = mems::GenericInterval<>]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector*>]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:982:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 982 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 983 | __gnu_cxx::__ops::__iter_equal_to_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = std::vector]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/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++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:982:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 982 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 983 | __gnu_cxx::__ops::__iter_equal_to_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = mems::GenericMatchList >*>]': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In member function 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector&, const std::vector&, const GappedAlignmentType&, Matrix >*> >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, boost::multi_array >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 923 | } | ^ ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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++/10/bits/stl_vector.h: In member function 'void mems::ProgressiveAligner::CreatePairwiseBPDistance(boost::multi_array&)': /usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 1665 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1666 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1665:19: 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++/10/bits/stl_algo.h:61, from /usr/include/c++/10/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++/10/bits/stl_heap.h:412:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 412 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:412:23: 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++/10/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++/10/bits/stl_algo.h: In member function 'void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In member function 'void mems::ProgressiveAligner::getAlignment(mems::IntervalList&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 121 | _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 -fdebug-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 -fdebug-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/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/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/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../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 cr .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 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 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-filesystem1.74-dev package exists. --> libboost-iostreams1.74-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 find debian -name "lib*.la" -delete 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_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libmems1' in '../libmems1_1.6.0+4725-9_armhf.deb'. dpkg-deb: building package 'libmems1-dbgsym' in '../libmems1-dbgsym_1.6.0+4725-9_armhf.deb'. dpkg-deb: building package 'libmems-dev' in '../libmems-dev_1.6.0+4725-9_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libmems_1.6.0+4725-9_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3782/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3782/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/3782 and its subdirectories I: Current time: Mon Aug 23 04:19:34 +14 2021 I: pbuilder-time-stamp: 1629641974