I: pbuilder: network access will be disabled during build
I: Current time: Wed May 10 05:31:01 -12 2023
I: pbuilder-time-stamp: 1683739861
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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: Signature made Mon Nov 16 21:02:37 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libmems_1.6.0+4725-9.dsc: no acceptable signature found
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/31848/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='5aaeb579b0444f72b296800be2af78a5'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='31848'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wVJCJ7n9/pbuilderrc_pJ3e --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wVJCJ7n9/b1 --logfile b1/build.log libmems_1.6.0+4725-9.dsc'
SUDO_GID='114'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux jtx1b 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/31848/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19329 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} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.5 MB of archives. After unpacking 282 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf d-shlibs all 0.104 [18.6 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf icu-devtools armhf 72.1-3 [183 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libboost1.74-dev armhf 1.74.0+ds1-20 [9510 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf libboost-filesystem1.74.0 armhf 1.74.0+ds1-20 [250 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf libboost-system1.74.0 armhf 1.74.0+ds1-20 [218 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libboost-system1.74-dev armhf 1.74.0+ds1-20 [219 kB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf libboost-filesystem1.74-dev armhf 1.74.0+ds1-20 [264 kB]
Get: 38 http://deb.debian.org/debian bookworm/main armhf libboost-filesystem-dev armhf 1.74.0.3 [4368 B]
Get: 39 http://deb.debian.org/debian bookworm/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-20 [432 kB]
Get: 40 http://deb.debian.org/debian bookworm/main armhf libicu-dev armhf 72.1-3 [10.1 MB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-20 [543 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf libboost-iostreams1.74-dev armhf 1.74.0+ds1-20 [247 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf libboost-iostreams-dev armhf 1.74.0.3 [4316 B]
Get: 44 http://deb.debian.org/debian bookworm/main armhf libboost-program-options1.74.0 armhf 1.74.0+ds1-20 [311 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf libboost-program-options1.74-dev armhf 1.74.0+ds1-20 [355 kB]
Get: 46 http://deb.debian.org/debian bookworm/main armhf libboost-program-options-dev armhf 1.74.0.3 [4340 B]
Get: 47 http://deb.debian.org/debian bookworm/main armhf libgenome0 armhf 1.3.11+svn20110227.4616-5 [102 kB]
Get: 48 http://deb.debian.org/debian bookworm/main armhf libgenome-dev armhf 1.3.11+svn20110227.4616-5 [179 kB]
Get: 49 http://deb.debian.org/debian bookworm/main armhf libmuscle1 armhf 3.7+4565-7 [201 kB]
Get: 50 http://deb.debian.org/debian bookworm/main armhf libmuscle-dev armhf 3.7+4565-7 [259 kB]
Get: 51 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get: 52 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB]
Get: 53 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get: 54 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
Fetched 41.5 MB in 4s (11.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19329 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_armhf.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_armhf.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_armhf.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_armhf.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_armhf.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_armhf.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../15-d-shlibs_0.104_all.deb ...
Unpacking d-shlibs (0.104) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/libmems-1.6.0+4725/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 <tille@debian.org>
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.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:429: AM_INIT_AUTOMAKE is expanded from...
configure.ac:54: the top level
configure.ac:66: warning: The macro `AM_PROG_LIBTOOL' is obsolete.
configure.ac:66: You should run autoupdate.
m4/libtool.m4:101: AM_PROG_LIBTOOL is expanded from...
configure.ac:66: the top level
configure.ac:70: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:70: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:70: the top level
configure.ac:92: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete.
configure.ac:92: You should run autoupdate.
./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/ac_cxx_namespaces.m4:12: AC_CXX_NAMESPACES is expanded from...
configure.ac:92: the top level
configure.ac:92: warning: The macro `AC_TRY_COMPILE' is obsolete.
configure.ac:92: You should run autoupdate.
./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/ac_cxx_namespaces.m4:12: AC_CXX_NAMESPACES is expanded from...
configure.ac:92: the top level
configure.ac:122: warning: 'AM_CONFIG_HEADER': this macro is obsolete.
configure.ac:122: You should use the 'AC_CONFIG_HEADERS' macro instead.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:745: AM_CONFIG_HEADER is expanded from...
configure.ac:122: the top level
configure.ac:128: warning: The macro `AC_HEADER_TIME' is obsolete.
configure.ac:128: You should run autoupdate.
./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
configure.ac:128: the top level
configure.ac:136: warning: AC_OUTPUT should be used without arguments.
configure.ac:136: You should run autoupdate.
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 one 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, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as 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
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checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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
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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 file... file
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checking how to recognize dependent libraries... pass_all
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checking how to associate runtime and link libraries... printf %s\n
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking for string.h... yes
checking for inttypes.h... yes
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checking for strings.h... yes
checking for sys/stat.h... yes
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checking for unistd.h... yes
checking for sys/time.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 egrep... (cached) /bin/grep -E
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 for boost/system/error_code.hpp... yes
checking for the Boost system library... yes
checking for boost/filesystem/path.hpp... yes
checking for the Boost filesystem library... (cached) yes
checking for boost/program_options.hpp... yes
checking for the Boost program_options library... (cached) 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 for sys/aio.h... no
checking for aio.h... 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 how to run the C preprocessor... gcc -E
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 -j3
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/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector<long long unsigned int>&) const' at MatchFinder.cpp:110:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector<long long unsigned int>&) const' at MatchFinder.cpp:123:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void mems::MatchFinder::FindMatchSeeds(const std::vector<long long unsigned int>&)' at MatchFinder.cpp:145:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void mems::MatchFinder::FindMatchSeeds()' at MatchFinder.cpp:132:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::bmer>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual boolean mems::MemorySML::Read(std::vector<mems::bmer>&, gnSeqI, gnSeqI)' at MemorySML.cpp:79:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from MemorySML.cpp:14:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Distance = int; _Tp = mems::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::MemorySML::Create(const genome::gnSequence&, uint64)' at MemorySML.cpp:54:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::MemorySML::Create(const genome::gnSequence&, uint64)' at MemorySML.cpp:54:6:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::SortedMerList::FindAll(const std::string&, std::vector<long long unsigned int>)' at SortedMerList.cpp:228:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::SortedMerList::FillSML(gnSeqI, std::vector<long long unsigned int>&)' at SortedMerList.cpp:578:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::bmer>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector<mems::bmer>&)' at SortedMerList.cpp:553:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector<mems::bmer>&)' at SortedMerList.cpp:563:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector<mems::bmer>&)' at SortedMerList.cpp:660:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector<mems::bmer>&)' at SortedMerList.cpp:662:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector<mems::bmer>&)' at SortedMerList.cpp:707:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector<mems::bmer>&)' at SortedMerList.cpp:709:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::bmer>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::RadixSort(std::vector<mems::bmer>&)' at FileSML.cpp:474:39:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::RadixSort(std::vector<mems::bmer>&)' at FileSML.cpp:484:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::RadixSort(std::vector<mems::bmer>&)' at FileSML.cpp:497:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'virtual void mems::FileSML::LoadFile(const std::string&)' at FileSML.cpp:107:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
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:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Distance = int; _Tp = mems::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:589:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:591:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:591:6:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:598:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:648:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:650:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::bmer; _Alloc = std::allocator<mems::bmer>]',
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:654:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:656:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)' at FileSML.cpp:656:6:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector<long long int>&, int)' at FileSML.cpp:258:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector<long long int>&, int)' at FileSML.cpp:259:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector<long long int>&, int)' at FileSML.cpp:272:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector<long long int>&, int)' at FileSML.cpp:273:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Create(const genome::gnSequence&, uint64)' at FileSML.cpp:344:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mems::bmer&, const mems::bmer&)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::bmer*, vector<mems::bmer> >; _Compare = bool (*)(const mems::bmer&, const mems::bmer&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void mems::FileSML::Create(const genome::gnSequence&, uint64)' at FileSML.cpp:344:6:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::bmer*, std::vector<mems::bmer> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void mems::MemHash::FindMatches(mems::MatchList&)' at MemHash.cpp:112:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o
In file included from /usr/include/c++/12/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++/12/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/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o
In file included from /usr/include/c++/12/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++/12/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 ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o
In file included from /usr/include/c++/12/vector:70,
from /usr/include/libGenome/gnGenomeSpec.h:21,
from /usr/include/libGenome/gnSequence.h:27,
from ../libMems/Islands.h:16:
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
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++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Distance = int; _Tp = pair<double, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::MoveScoreHeapComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/libGenome/gnGenomeSpec.h:21,
from /usr/include/libGenome/gnSequence.h:27,
from ../libMems/Aligner.h:16:
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::Island&}; _Tp = mems::Island; _Alloc = std::allocator<mems::Island>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::Island>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::Island; _Alloc = std::allocator<mems::Island>]',
inlined from 'void mems::simpleFindIslands(IntervalList&, uint, std::vector<Island>&)' at Islands.cpp:78:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::Island*, std::vector<mems::Island> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector<genome::gnSequence*>&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:934:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GappedAlignment&}; _Tp = mems::GappedAlignment; _Alloc = std::allocator<mems::GappedAlignment>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::GappedAlignment>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' changed in GCC 7.1
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::addUnalignedIntervals(IntervalList&, std::set<unsigned int>, std::vector<long long unsigned int>)' at Islands.cpp:244:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::addUnalignedIntervals(IntervalList&, std::set<unsigned int>, std::vector<long long unsigned int>)' at Islands.cpp:294:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::CreateGapSearchList(std::vector<LCB>&, const std::vector<genome::gnSequence*>&, std::vector<std::vector<long long int, std::allocator<long long int> > >&, boolean)' at Aligner.cpp:775:32,
inlined from 'void mems::CreateGapSearchList(std::vector<LCB>&, const std::vector<genome::gnSequence*>&, std::vector<std::vector<long long int, std::allocator<long long int> > >&, boolean)' at Aligner.cpp:720:6:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::CreateGapSearchList(std::vector<LCB>&, const std::vector<genome::gnSequence*>&, std::vector<std::vector<long long int, std::allocator<long long int> > >&, boolean)' at Aligner.cpp:776:32,
inlined from 'void mems::CreateGapSearchList(std::vector<LCB>&, const std::vector<genome::gnSequence*>&, std::vector<std::vector<long long int, std::allocator<long long int> > >&, boolean)' at Aligner.cpp:720:6:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GappedAlignment; _Alloc = std::allocator<mems::GappedAlignment>]',
inlined from 'void mems::simpleFindBackbone(IntervalList&, uint, uint, std::vector<GappedAlignment>&)' at Islands.cpp:143:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GappedAlignment*, std::vector<mems::GappedAlignment> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GappedAlignment; _Alloc = std::allocator<mems::GappedAlignment>]',
inlined from 'void mems::simpleFindBackbone(IntervalList&, uint, uint, std::vector<GappedAlignment>&)' at Islands.cpp:188:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GappedAlignment*, std::vector<mems::GappedAlignment> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:311:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:313:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:315:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::LCB*, vector<mems::LCB> >; _ForwardIterator = mems::LCB*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)' at Aligner.cpp:1128:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v2(IntervalList&, std::vector<long long int, std::allocator<long long int> >&, std::vector<LCB>&)' at Aligner.cpp:683:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v2(IntervalList&, std::vector<long long int, std::allocator<long long int> >&, std::vector<LCB>&)' at Aligner.cpp:683:7:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v2(IntervalList&, std::vector<long long int, std::allocator<long long int> >&, std::vector<LCB>&)' at Aligner.cpp:700:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v2(IntervalList&, std::vector<long long int, std::allocator<long long int> >&, std::vector<LCB>&)' at Aligner.cpp:700:6:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void mems::computeLCBAdjacencies_v2(std::vector<GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*> >&, std::vector<long long int, std::allocator<long long int> >&, std::vector<LCB>&)' at Aligner.cpp:635:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::LCB*, std::vector<mems::LCB> >; _ForwardIterator = mems::LCB*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::LCB*, vector<mems::LCB> >; _ForwardIterator = mems::LCB*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::LCB*, vector<mems::LCB> >; _ForwardIterator = mems::LCB*; _Tp = mems::LCB]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'void mems::Aligner::consistencyCheck(uint, std::vector<mems::LCB>&, std::vector<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, std::vector<long long int, std::allocator<long long int> >&)' at Aligner.cpp:1586:26:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:311:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:313:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:315:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, boolean, std::ostream*)' at Aligner.cpp:2130:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::string)' at Aligner.cpp:2273:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1
In file included from /usr/include/c++/12/vector:70,
from ../libMems/Matrix.h:19,
from ../libMems/NumericMatrix.h:16,
from ../libMems/MuscleInterface.h:16,
from MuscleInterface.cpp:13:
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:451:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:462:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:473:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:469:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:552:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:576:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:599:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector<genome::gnSequence*>&)' at MuscleInterface.cpp:592:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o
In file included from /usr/include/c++/12/vector:70,
from ../libMems/RepeatMatch.h:18,
from RepeatMatch.cpp:13:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1
In file included from /usr/include/c++/12/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++/12/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/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o
In file included from /usr/include/c++/12/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++/12/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/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
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:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../libMems/AbstractMatch.h:17:
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:311:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:313:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:315:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector<genome::gnSequence*>&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:934:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const' at ../libMems/MatchProjectionAdapter.h:118:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<UngappedLocalAlignment<HybridAbstractMatch<> >*, std::allocator<UngappedLocalAlignment<HybridAbstractMatch<> >*> >]' at Backbone.cpp:38:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<UngappedLocalAlignment<HybridAbstractMatch<> >*, std::allocator<UngappedLocalAlignment<HybridAbstractMatch<> >*> >]' at Backbone.cpp:39:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<UngappedLocalAlignment<HybridAbstractMatch<> >*, std::allocator<UngappedLocalAlignment<HybridAbstractMatch<> >*> >]' at Backbone.cpp:41:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<CompactGappedAlignment<>*>]' at Backbone.cpp:38:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<CompactGappedAlignment<>*>]' at Backbone.cpp:39:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::getBpList(MatchVector&, uint, std::vector<long long unsigned int>&) [with MatchVector = std::vector<CompactGappedAlignment<>*>]' at Backbone.cpp:41:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:138:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::LCB>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o
In file included from /usr/include/c++/12/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++/12/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++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
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:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Distance = int; _Tp = pair<double, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::MoveScoreHeapComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../libMems/AbstractMatch.h:17:
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
189 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_equal_to_iter]':
/usr/include/c++/12/bits/stl_algo.h:902:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
902 | __unique(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:902:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
175 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]':
/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator' changed in GCC 7.1
739 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]',
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:287:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../libMems/AbstractMatch.h:18,
from ../libMems/GreedyBreakpointElimination.h:8,
from GreedyBreakpointElimination.cpp:6:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:195:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:213:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:215:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:221:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<MatchProjectionAdapter*>]' at ../libMems/GreedyBreakpointElimination.h:223:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::makeAllPairwiseGenomeHSS(IntervalList&, std::vector<CompactGappedAlignment<>*>&, std::vector<CompactGappedAlignment<>*>&, pairwise_genome_hss_t&, const HssDetector*)' at Backbone.cpp:350:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const' at ../libMems/PairwiseMatchAdapter.h:90:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const' at ../libMems/PairwiseMatchAdapter.h:91:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../libMems/AbstractMatch.h:17:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const' at ../libMems/PairwiseMatchAdapter.h:90:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const' at ../libMems/PairwiseMatchAdapter.h:91:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::HybridAbstractMatch<FIXED_SEQ_COUNT, int64Alloc, uintAlloc>::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator<long long int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/HybridAbstractMatch.h:197:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, unsigned int>}; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, unsigned int>}; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::LCB>::iterator' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:311:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void mems::unalignIslands(IntervalList&, std::vector<CompactGappedAlignment<>*>&, std::vector<std::vector<UngappedLocalAlignment<HybridAbstractMatch<> >*, std::allocator<UngappedLocalAlignment<HybridAbstractMatch<> >*> > >&)' at Backbone.cpp:798:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::applyAncestralBreakpoints(const std::vector<SuperInterval>&, std::vector<MatchPtrType>&, uint, Manipulator&) [with T = AbstractMatch*; Manipulator = GenericMatchSeqManipulator<>]' at ProgressiveAligner.cpp:265:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:182:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:187:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]' at ../libMems/SparseAbstractMatch.h:129:16:
/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1530 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::MoveScoreHeapComparator>]':
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
In function 'void std::make_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Compare = mems::MoveScoreHeapComparator]',
inlined from 'int64 mems::greedyBreakpointElimination_v4(std::vector<LCB>&, std::vector<double>&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = SimpleBreakpointScorer]' at ../libMems/GreedyBreakpointElimination.h:695:16:
/usr/include/c++/12/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
413 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]',
inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; <template-parameter-2-2> = void; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]' at /usr/include/c++/12/bits/stl_vector.h:1481:22,
inlined from 'int64 mems::greedyBreakpointElimination_v4(std::vector<LCB>&, std::vector<double>&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = SimpleBreakpointScorer]' at ../libMems/GreedyBreakpointElimination.h:727:21:
/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator' changed in GCC 7.1
1779 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1780 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
In function 'void std::make_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Compare = mems::MoveScoreHeapComparator]',
inlined from 'double mems::greedySearch(SearchScorer&) [with SearchScorer = EvenFasterSumOfPairsBreakpointScorer]' at ../libMems/GreedyBreakpointElimination.h:794:16:
/usr/include/c++/12/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
413 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]',
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<T>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:287:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<T>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<T>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<T>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<T>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void mems::chooseNextAlignmentPair(PhyloTree<AlignmentTreeNode>&, node_id_t&, node_id_t&, node_id_t&)' at ProgressiveAligner.cpp:3127:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void mems::chooseNextAlignmentPair(PhyloTree<AlignmentTreeNode>&, node_id_t&, node_id_t&, node_id_t&)' at ProgressiveAligner.cpp:3135:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:311:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:313:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:315:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::LCB>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:195:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:213:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:215:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:221:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:223:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:223:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector<genome::gnSequence*>&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:934:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::GenericInterval<GappedBaseImpl>::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector<genome::gnSequence*>&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<mems::SparseAbstractMatch<> >]' at ../libMems/Interval.h:934:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array<double, 2>, boost::multi_array<double, 2>, std::vector<mems::LcbTrackingMatch<mems::AbstractMatch*>*>, mems::PairwiseLCBMatrix&, std::vector<unsigned int>&, std::vector<unsigned int>&, boost::multi_array<double, 3>&, boost::multi_array<unsigned int, 3>&, size_t, size_t, size_t, size_t)' at GreedyBreakpointElimination.cpp:368:18:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*; _Tp = mems::SuperInterval]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >; _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]' at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const mems::SuperInterval*, vector<mems::SuperInterval> >; _ForwardIterator = mems::SuperInterval*; _Tp = mems::SuperInterval]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'mems::AlignmentTreeNode::AlignmentTreeNode(const mems::AlignmentTreeNode&)' at ../libMems/ProgressiveAligner.h:36:7:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::AlignmentTreeNode&}; _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]',
inlined from 'void PhyloTree<T>::push_back(T&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:57:41,
inlined from 'node_id_t mems::createAlignmentTreeRoot(PhyloTree<AlignmentTreeNode>&, node_id_t, node_id_t)' at ProgressiveAligner.cpp:3189:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::AlignmentTreeNode*, std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]',
inlined from 'void PhyloTree<T>::readTree(std::istream&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:173:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::AlignmentTreeNode*, std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]',
inlined from 'void PhyloTree<T>::readTree(std::istream&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:191:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::AlignmentTreeNode*, std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]',
inlined from 'void PhyloTree<T>::readTree(std::istream&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:217:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::AlignmentTreeNode*, std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator<mems::AlignmentTreeNode>]',
inlined from 'void PhyloTree<T>::readTree(std::istream&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:235:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::AlignmentTreeNode*, std::vector<mems::AlignmentTreeNode, std::allocator<mems::AlignmentTreeNode> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::SuperInterval&}; _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::SuperInterval>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::applyAncestralBreakpoints(const std::vector<SuperInterval>&, std::vector<MatchPtrType>&, uint, Manipulator&) [with T = SuperInterval; Manipulator = SuperIntervalManipulator]' at ProgressiveAligner.cpp:265:6,
inlined from 'void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_t)' at ProgressiveAligner.cpp:543:29:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]',
inlined from 'void mems::SuperIntervalManipulator::AddCopy(ContainerType&, const mems::SuperInterval&) const [with ContainerType = std::vector<mems::SuperInterval>]' at ../libMems/ProgressiveAligner.h:553:77,
inlined from 'void mems::applyBreakpoints(std::vector<long long unsigned int>&, std::vector<MatchPtrType>&, Maniplator&) [with T = SuperInterval; Maniplator = SuperIntervalManipulator]' at ../libMems/ProgressiveAligner.h:592:16,
inlined from 'void mems::applyAncestralBreakpoints(const std::vector<SuperInterval>&, std::vector<MatchPtrType>&, uint, Manipulator&) [with T = SuperInterval; Manipulator = SuperIntervalManipulator]' at ProgressiveAligner.cpp:266:18,
inlined from 'void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_t)' at ProgressiveAligner.cpp:543:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]',
inlined from 'void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_t)' at ProgressiveAligner.cpp:552:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]',
inlined from 'void mems::makeAlignmentTree(PhyloTree<AlignmentTreeNode>&, MatchListType&, std::vector<unsigned int>&) [with MatchListType = GenericIntervalList<>]' at ProgressiveAligner.cpp:3502:45:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::SuperInterval; _Alloc = std::allocator<mems::SuperInterval>]',
inlined from 'void mems::makeAlignmentTree(PhyloTree<AlignmentTreeNode>&, MatchListType&, std::vector<unsigned int>&) [with MatchListType = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ProgressiveAligner.cpp:3502:45:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::SuperInterval*, std::vector<mems::SuperInterval> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]',
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:287:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]',
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:287:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]',
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<GenericInterval<>*>]' at ../libMems/GreedyBreakpointElimination.h:287:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<GenericInterval<>*>]' at ../libMems/GreedyBreakpointElimination.h:292:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<GenericInterval<>*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::LCB*, vector<mems::LCB> >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<LCB>&) [with MatchVector = std::vector<GenericInterval<>*>]' at ../libMems/GreedyBreakpointElimination.h:309:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:223:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]',
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:224:49:
/usr/include/c++/12/bits/stl_algo.h:945:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
945 | return std::__unique(__first, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
946 | __gnu_cxx::__ops::__iter_equal_to_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:225:19:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void mems::filterMatches_v2(std::vector<LCB>&, std::vector<MatchPtrType>&, std::vector<double>&, MatchVector&) [with MatchVector = std::vector<AbstractMatch*>]' at ../libMems/GreedyBreakpointElimination.h:381:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:223:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<long long unsigned int*, vector<long long unsigned int> >]',
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:224:49:
/usr/include/c++/12/bits/stl_algo.h:945:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
945 | return std::__unique(__first, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
946 | __gnu_cxx::__ops::__iter_equal_to_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]',
inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:225:19:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void mems::filterMatches_v2(std::vector<LCB>&, std::vector<MatchPtrType>&, std::vector<double>&, MatchVector&) [with MatchVector = GenericMatchList<UngappedLocalAlignment<HybridAbstractMatch<> >*>]' at ../libMems/GreedyBreakpointElimination.h:381:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::pairwiseAnchorSearch(mems::MatchList&, mems::Match*, mems::Match*, const mems::AbstractMatch*, uint, uint)' at ProgressiveAligner.cpp:605:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:715:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:716:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:724:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:725:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:787:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:788:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:797:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:798:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:812:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:813:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:822:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector<unsigned int>&, const std::vector<unsigned int>&, const GappedAlignmentType&, Matrix<mems::GenericMatchList<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, Matrix<std::vector<std::pair<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >&, boost::multi_array<std::vector<std::vector<long long int> >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:823:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::make_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, unsigned int>*, vector<pair<double, unsigned int> > >; _Compare = mems::MoveScoreHeapComparator]',
inlined from 'int64 mems::greedyBreakpointElimination_v4(std::vector<LCB>&, std::vector<double>&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = GreedyRemovalScorer]' at ../libMems/GreedyBreakpointElimination.h:695:16,
inlined from 'void mems::ProgressiveAligner::CreatePairwiseBPDistance(boost::multi_array<double, 2>&)' at ProgressiveAligner.cpp:3433:52:
/usr/include/c++/12/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
413 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]',
inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >; <template-parameter-2-2> = void; _Tp = std::pair<double, unsigned int>; _Alloc = std::allocator<std::pair<double, unsigned int> >]' at /usr/include/c++/12/bits/stl_vector.h:1481:22,
inlined from 'int64 mems::greedyBreakpointElimination_v4(std::vector<LCB>&, std::vector<double>&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = GreedyRemovalScorer]' at ../libMems/GreedyBreakpointElimination.h:727:21,
inlined from 'void mems::ProgressiveAligner::CreatePairwiseBPDistance(boost::multi_array<double, 2>&)' at ProgressiveAligner.cpp:3433:52:
/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector<std::pair<double, unsigned int> >::iterator' changed in GCC 7.1
1779 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1780 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, unsigned int>*, std::vector<std::pair<double, unsigned int> > >' changed in GCC 7.1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)' at ProgressiveAligner.cpp:2477:14:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)' at ProgressiveAligner.cpp:2478:14:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from HomologyHMM/algebras.cc:27:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from HomologyHMM/dptables.h:43,
from HomologyHMM/homology.h:27,
from HomologyHMM/homology.cc:24:
/usr/include/c++/12/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 HomologyHMM/homology.h:28:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Forward(HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:319:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
319 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
321 | register bfloat iTempProb[1];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
417 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
419 | register bfloat iTempProb[3];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Viterbi_recurse(HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
565 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
567 | register bfloat iTempProb[1];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)':
HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
673 | register double iTempResult[1];
| ^~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void mems::ProgressiveAligner::getAlignment(mems::IntervalList&)' at ProgressiveAligner.cpp:3771:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/backward/hashtable.h:62,
from /usr/include/c++/12/ext/hash_map:64:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void SimplePath::addEdge(int, double, std::vector<int>&, int, int)' at HomologyHMM/homology.cc:248:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from HomologyHMM/dptables.h:43,
from HomologyHMM/homology.h:27,
from HomologyHMM/homologymain.cc:21:
/usr/include/c++/12/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 HomologyHMM/homology.h:28:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o
dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO':
dmSML/aPOSIXaio.c:115:28: 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:489,
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:202:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **'
202 | extern int __REDIRECT_NTH (aio_suspend,
| ^~~~~~~~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/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 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o
dmSML/util.c: In function 'removeFile':
dmSML/util.c:126:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
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 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/arm-linux-gnueabihf RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/12/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/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/12/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/12/../../../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 -j3 check "TESTSUITEFLAGS=-j3 --verbose" 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/bash ../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-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-deb: building package 'libmems1' in '../libmems1_1.6.0+4725-9_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../libmems_1.6.0+4725-9_armhf.buildinfo
dpkg-genchanges --build=binary -O../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: 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/31848 and its subdirectories
I: Current time: Wed May 10 05:42:13 -12 2023
I: pbuilder-time-stamp: 1683740533