sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org

+==============================================================================+
| progressivemauve 1.2.0+4713+dfsg-4 (armel)   Tue, 11 Jun 2019 20:45:29 +0000 |
+==============================================================================+

Package: progressivemauve
Version: 1.2.0+4713+dfsg-4
Source Version: 1.2.0+4713+dfsg-4
Distribution: unstable
Machine Architecture: amd64
Host Architecture: armel
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-0122609e-a43d-4118-b74e-1f6b4cbe6a9c' with '<<CHROOT>>'

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| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [210 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-11-1418.40.pdiff [817 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-11-1418.40.pdiff [1586 B]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-11-1418.40.pdiff [817 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-11-1418.40.pdiff [1586 B]
Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [8006 kB]
Fetched 8274 kB in 2s (4428 kB/s)
Reading package lists...
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Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

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| Fetch source files                                                           |
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Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'progressivemauve' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/progressivemauve.git
Please use:
git clone https://salsa.debian.org/med-team/progressivemauve.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 116 kB of source archives.
Get:1 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (dsc) [2300 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (tar) [96.1 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (diff) [17.7 kB]
Fetched 116 kB in 0s (0 B/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/progressivemauve-aQEBMX/progressivemauve-1.2.0+4713+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/progressivemauve-aQEBMX' with '<<BUILDDIR>>'

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| Install crossbuild-essential                                                 |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64
Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-NGQHVR/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release [957 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Sources [359 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Packages [453 B]
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Reading package lists...
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Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  binutils-arm-linux-gnueabi cpp-8-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel dpkg-cross file
  g++-8-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-8-arm-linux-gnueabi
  gcc-8-arm-linux-gnueabi-base gcc-8-cross-base gcc-arm-linux-gnueabi
  libasan5-armel-cross libatomic1-armel-cross libc6-armel-cross
  libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl
  libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl
  libgcc-8-dev-armel-cross libgcc1-armel-cross libgomp1-armel-cross libicu63
  libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libstdc++-8-dev-armel-cross libstdc++6-armel-cross libubsan1-armel-cross
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev-armel-cross sensible-utils ucf
Suggested packages:
  binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc
  libstdc++6-8-dbg-armel-cross libgcc1-dbg-armel-cross
  libgomp1-dbg-armel-cross libitm1-dbg-armel-cross libatomic1-dbg-armel-cross
  libasan5-dbg-armel-cross liblsan0-dbg-armel-cross libtsan0-dbg-armel-cross
  libubsan1-dbg-armel-cross libmpx2-dbg-armel-cross
  libquadmath0-dbg-armel-cross manpages-dev autoconf automake libtool flex
  bison gdb-arm-linux-gnueabi gcc-doc libyaml-shell-perl
Recommended packages:
  libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl
The following NEW packages will be installed:
  binutils-arm-linux-gnueabi cpp-8-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel dpkg-cross file
  g++-8-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-8-arm-linux-gnueabi
  gcc-8-arm-linux-gnueabi-base gcc-8-cross-base gcc-arm-linux-gnueabi
  libasan5-armel-cross libatomic1-armel-cross libc6-armel-cross
  libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl
  libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl
  libgcc-8-dev-armel-cross libgcc1-armel-cross libgomp1-armel-cross libicu63
  libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libstdc++-8-dev-armel-cross libstdc++6-armel-cross libubsan1-armel-cross
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev-armel-cross sbuild-build-depends-core-dummy:armel
  sensible-utils ucf
0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.8 MB of archives.
After this operation, 154 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB]
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Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.31.1-16 [2832 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabi-base amd64 8.3.0-7cross1 [191 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-arm-linux-gnueabi amd64 8.3.0-7cross1 [6545 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:8.3.0-1 [16.5 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.28-10cross2 [1190 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armel-cross all 1:8.3.0-7cross1 [38.4 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 8.3.0-7cross1 [65.6 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 8.3.0-7cross1 [8812 B]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 8.3.0-7cross1 [288 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 8.3.0-7cross1 [311 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 8.3.0-7cross1 [102 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-armel-cross all 8.3.0-7cross1 [601 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabi amd64 8.3.0-7cross1 [6970 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:8.3.0-1 [1460 B]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 4.19.28-2cross2 [1228 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.28-10cross2 [2184 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-armel-cross all 8.3.0-7cross1 [1543 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-arm-linux-gnueabi amd64 8.3.0-7cross1 [7123 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:8.3.0-1 [1176 B]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.6 [6568 B]
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Setting up libfile-homedir-perl (1.004-1) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ...
Setting up liblocale-gettext-perl (1.07-3+b4) ...
Setting up libgomp1-armel-cross (8.3.0-7cross1) ...
Setting up libatomic1-armel-cross (8.3.0-7cross1) ...
Setting up libgcc1-armel-cross (1:8.3.0-7cross1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up libstdc++6-armel-cross (8.3.0-7cross1) ...
Setting up libxml-sax-perl (1.00+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libasan5-armel-cross (8.3.0-7cross1) ...
Setting up libubsan1-armel-cross (8.3.0-7cross1) ...
Setting up libxml-libxml-perl (2.0134+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libgcc-8-dev-armel-cross (8.3.0-7cross1) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up gcc-8-arm-linux-gnueabi (8.3.0-7cross1) ...
Setting up libstdc++-8-dev-armel-cross (8.3.0-7cross1) ...
Setting up libconfig-auto-perl (0.44-1) ...
Setting up gcc-arm-linux-gnueabi (4:8.3.0-1) ...
Setting up libdebian-dpkgcross-perl (2.6.15-3) ...
Setting up g++-8-arm-linux-gnueabi (8.3.0-7cross1) ...
Setting up g++-arm-linux-gnueabi (4:8.3.0-1) ...
Setting up dpkg-cross (2.6.15-3) ...
Setting up crossbuild-essential-armel (12.6) ...
Setting up sbuild-build-depends-core-dummy:armel (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armel included in any)

Setup apt archive
-----------------

dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<<BUILDDIR>>/resolver-NGQHVR/apt_archive/sbuild-build-depends-essential-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release [963 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Sources [481 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Packages [569 B]
Fetched 2013 B in 0s (113 kB/s)
Reading package lists...
Reading package lists...

Install essential build dependencies (apt-based resolver)
---------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-essential-dummy:armel
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 840 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 840 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-essential-dummy:armel.
(Reading database ... 15002 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_armel.deb ...
Unpacking sbuild-build-depends-essential-dummy:armel (0.invalid.0) ...
Setting up sbuild-build-depends-essential-dummy:armel (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev
Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev
dpkg-deb: building package 'sbuild-build-depends-progressivemauve-dummy' in '/<<BUILDDIR>>/resolver-NGQHVR/apt_archive/sbuild-build-depends-progressivemauve-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-progressivemauve-dummy
dpkg-scanpackages: info: Wrote 3 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release [963 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Sources [703 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Packages [779 B]
Fetched 2445 B in 0s (118 kB/s)
Reading package lists...
Reading package lists...

Install progressivemauve build dependencies (apt-based resolver)
----------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armel gettext
  gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
  libasan5:armel libatomic1:armel libboost-dev:armel
  libboost-filesystem-dev:armel libboost-filesystem1.67-dev:armel
  libboost-filesystem1.67.0:armel libboost-iostreams-dev:armel
  libboost-iostreams1.67-dev:armel libboost-iostreams1.67.0:armel
  libboost-program-options-dev:armel libboost-program-options1.67-dev:armel
  libboost-program-options1.67.0:armel libboost-regex1.67-dev:armel
  libboost-regex1.67.0:armel libboost-system-dev:armel
  libboost-system1.67-dev:armel libboost-system1.67.0:armel
  libboost1.67-dev:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-dev:armel
  libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armel
  libgcc1:armel libgenome-dev:armel libgenome0:armel libglib2.0-0
  libgomp1:armel libicu-dev:armel libicu63:armel libmems-dev:armel
  libmems1:armel libmuscle-dev:armel libmuscle1:armel libncurses6 libpipeline1
  libsigsegv2 libstdc++-8-dev:armel libstdc++6:armel libtool libubsan1:armel
  libuchardet0 linux-libc-dev:armel m4 man-db pkgconf po-debconf zlib1g:armel
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  libboost-doc:armel libboost1.67-doc:armel libboost-atomic1.67-dev:armel
  libboost-chrono1.67-dev:armel libboost-container1.67-dev:armel
  libboost-context1.67-dev:armel libboost-coroutine1.67-dev:armel
  libboost-date-time1.67-dev:armel libboost-exception1.67-dev:armel
  libboost-fiber1.67-dev:armel libboost-graph1.67-dev:armel
  libboost-graph-parallel1.67-dev:armel libboost-locale1.67-dev:armel
  libboost-log1.67-dev:armel libboost-math1.67-dev:armel
  libboost-mpi1.67-dev:armel libboost-mpi-python1.67-dev:armel
  libboost-numpy1.67-dev:armel libboost-python1.67-dev:armel
  libboost-random1.67-dev:armel libboost-serialization1.67-dev:armel
  libboost-signals1.67-dev:armel libboost-stacktrace1.67-dev:armel
  libboost-test1.67-dev:armel libboost-thread1.67-dev:armel
  libboost-timer1.67-dev:armel libboost-type-erasure1.67-dev:armel
  libboost-wave1.67-dev:armel libboost1.67-tools-dev:armel
  libmpfrc++-dev:armel libntl-dev:armel glibc-doc:armel libc-l10n:armel
  locales:armel manpages-dev:armel icu-doc:armel libstdc++-8-doc:armel
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx libidn2-0:armel libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armel gettext
  gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
  libasan5:armel libatomic1:armel libboost-dev:armel
  libboost-filesystem-dev:armel libboost-filesystem1.67-dev:armel
  libboost-filesystem1.67.0:armel libboost-iostreams-dev:armel
  libboost-iostreams1.67-dev:armel libboost-iostreams1.67.0:armel
  libboost-program-options-dev:armel libboost-program-options1.67-dev:armel
  libboost-program-options1.67.0:armel libboost-regex1.67-dev:armel
  libboost-regex1.67.0:armel libboost-system-dev:armel
  libboost-system1.67-dev:armel libboost-system1.67.0:armel
  libboost1.67-dev:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-dev:armel
  libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armel
  libgcc1:armel libgenome-dev:armel libgenome0:armel libglib2.0-0
  libgomp1:armel libicu-dev:armel libicu63:armel libmems-dev:armel
  libmems1:armel libmuscle-dev:armel libmuscle1:armel libncurses6 libpipeline1
  libsigsegv2 libstdc++-8-dev:armel libstdc++6:armel libtool libubsan1:armel
  libuchardet0 linux-libc-dev:armel m4 man-db pkgconf po-debconf
  sbuild-build-depends-progressivemauve-dummy:armel zlib1g:armel
0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded.
Need to get 49.5 MB of archives.
After this operation, 323 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ sbuild-build-depends-progressivemauve-dummy 0.invalid.0 [936 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-2 [1259 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main armel gcc-8-base armel 8.3.0-7 [191 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 icu-devtools amd64 63.2-2 [189 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main armel libgcc1 armel 1:8.3.0-7 [38.4 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.28-10 [2399 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 8.3.0-7 [325 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 8.3.0-7 [317 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 8.3.0-7 [8948 B]
Get:36 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 8.3.0-7 [67.1 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 8.3.0-7 [103 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main armel libgcc-8-dev armel 8.3.0-7 [604 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 4.19.37-3 [1167 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.28-10 [2185 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-8-dev armel 8.3.0-7 [1571 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main armel libboost1.67-dev armel 1.67.0-13 [8386 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main armel libboost-dev armel 1.67.0.1 [3860 B]
Get:44 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67.0 armel 1.67.0-13 [229 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67.0 armel 1.67.0-13 [255 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67-dev armel 1.67.0-13 [231 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67-dev armel 1.67.0-13 [262 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem-dev armel 1.67.0.1 [3684 B]
Get:49 http://debian.oregonstate.edu/debian unstable/main armel libicu63 armel 63.2-2 [7979 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67.0 armel 1.67.0-13 [431 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main armel libicu-dev armel 63.2-2 [8922 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67-dev armel 1.67.0-13 [533 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.6-9 [44.5 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-1 [86.5 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67.0 armel 1.67.0-13 [245 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67-dev armel 1.67.0-13 [254 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams-dev armel 1.67.0.1 [3632 B]
Get:58 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67.0 armel 1.67.0-13 [331 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67-dev armel 1.67.0-13 [380 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options-dev armel 1.67.0.1 [3656 B]
Get:61 http://debian.oregonstate.edu/debian unstable/main armel libboost-system-dev armel 1.67.0.1 [3788 B]
Get:62 http://debian.oregonstate.edu/debian unstable/main armel libgenome0 armel 1.3.11+svn20110227.4616-2 [96.5 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main armel libgenome-dev armel 1.3.11+svn20110227.4616-2 [173 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main armel libmuscle1 armel 3.7+4565-6 [200 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main armel libmems1 armel 1.6.0+4725-8+b1 [525 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main armel libmuscle-dev armel 3.7+4565-6 [256 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main armel libmems-dev armel 1.6.0+4725-8+b1 [822 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 pkgconf amd64 1.6.0-1 [66.6 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 49.5 MB in 1s (36.1 MB/s)
Selecting previously unselected package libbsd0:amd64.
(Reading database ... 15002 files and directories currently installed.)
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Unpacking libbsd0:amd64 (0.9.1-2) ...
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Unpacking bsdmainutils (11.1.2+b1) ...
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Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ...
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Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ...
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+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.7 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armel-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armel-cross_8.3.0-7cross1 linux-libc-dev_4.19.37-3
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-arm-linux-gnueabi_2.31.1-16 binutils-common_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-7 cpp-8-arm-linux-gnueabi_8.3.0-7cross1 cpp-arm-linux-gnueabi_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-armel_12.6 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.45.2-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1 g++-8_8.3.0-7 g++-8-arm-linux-gnueabi_8.3.0-7cross1 g++-arm-linux-gnueabi_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-7 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libgenome-dev_1.3.11+svn20110227.4616-2 libgenome0_1.3.11+svn20110227.4616-2 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-3 libgomp1_8.3.0-7 libgomp1-armel-cross_8.3.0-7cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-7 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-7 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmems-dev_1.6.0+4725-8+b1 libmems1_1.6.0+4725-8+b1 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-7 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_8.3.0-7 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.2-1 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armel-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armel-cross_8.3.0-7cross1 libsystemd0_241-5 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libubsan1-armel-cross_8.3.0-7cross1 libuchardet0_0.0.6-3 libudev1_241-5 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-3 linux-libc-dev-armel-cross_4.19.28-2cross2 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pkgconf_1.6.0-1 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-progressivemauve-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec  4 09:10:58 2018 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./progressivemauve_1.2.0+4713+dfsg-4.dsc
dpkg-source: info: extracting progressivemauve in /<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg
dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg.orig.tar.xz
dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_build.patch
dpkg-source: info: applying do_not_build_static_binaries.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying use-native-getopt.patch
dpkg-source: info: applying adapt-to-unversioned-libs.patch
dpkg-source: info: applying fix_FTBFS_boost1.67.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.armel
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=helmut
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1003
SCHROOT_GROUP=helmut
SCHROOT_SESSION_ID=unstable-amd64-sbuild-0122609e-a43d-4118-b74e-1f6b4cbe6a9c
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package progressivemauve
dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armel
 fakeroot debian/rules clean
dh clean
   dh_clean
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
configure.ac:21: installing 'config/compile'
configure.ac:9: installing 'config/config.guess'
configure.ac:9: installing 'config/config.sub'
configure.ac:11: installing 'config/install-sh'
configure.ac:11: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/Makefile.am: installing 'config/depcomp'
src/Makefile.am:51: warning: variable 'EXTRA_mauveStatic_SOURCES' is defined but no program or
src/Makefile.am:51: library has 'mauveStatic' as canonical name (possible typo)
src/Makefile.am:49: warning: variable 'mauveStatic_SOURCES' is defined but no program or
src/Makefile.am:49: library has 'mauveStatic' as canonical name (possible typo)
src/Makefile.am:160: warning: variable 'progressiveMauveStatic_SOURCES' is defined but no program or
src/Makefile.am:160: library has 'progressiveMauveStatic' as canonical name (possible typo)
src/Makefile.am:50: warning: variable 'mauveStatic_LDADD' is defined but no program or
src/Makefile.am:50: library has 'mauveStatic' as canonical name (possible typo)
src/Makefile.am:161: warning: variable 'progressiveMauveStatic_LDADD' is defined but no program or
src/Makefile.am:161: library has 'progressiveMauveStatic' as canonical name (possible typo)
src/Makefile.am:52: warning: variable 'mauveStatic_DEPENDENCIES' is defined but no program or
src/Makefile.am:52: library has 'mauveStatic' as canonical name (possible typo)
   dh_auto_configure -a
	./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --libexecdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi
configure: WARNING: unrecognized options: --disable-maintainer-mode
configure: loading site script /etc/dpkg-cross/cross-config.armel
checking build system type... x86_64-pc-linux-gnu
checking host system type... arm-unknown-linux-gnueabi
checking target system type... arm-unknown-linux-gnueabi
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for arm-linux-gnueabi-strip... arm-linux-gnueabi-strip
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc
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... yes
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether arm-linux-gnueabi-gcc accepts -g... yes
checking for arm-linux-gnueabi-gcc option to accept ISO C89... none needed
checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of arm-linux-gnueabi-gcc... none
checking for arm-linux-gnueabi-g++... arm-linux-gnueabi-g++
checking whether we are using the GNU C++ compiler... yes
checking whether arm-linux-gnueabi-g++ accepts -g... yes
checking dependency style of arm-linux-gnueabi-g++... none
checking whether ln -s works... yes
checking how to run the C preprocessor... arm-linux-gnueabi-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for getopt_long... yes
checking for getopt... yes
checking for arm-linux-gnueabi-pkg-config... /usr/bin/arm-linux-gnueabi-pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for DEPS... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether time.h and sys/time.h may both be included... yes
checking for memset... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
checking whether arm-linux-gnueabi-gcc needs -traditional... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
   dh_auto_build -a
	make -j1
make[1]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
Making all in src
make[2]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make  all-am
make[3]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveAligner.o mauveAligner.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from mauveAligner.cpp:30:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl;
                                                ^~~~~~~~
mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
   cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl;
                                                                      ^~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/MatchFinder.h:17,
                 from /usr/include/libMems/MemHash.h:20,
                 from mauveAligner.cpp:22:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Match.h:20,
                 from /usr/include/libMems/MatchFinder.h:17,
                 from /usr/include/libMems/MemHash.h:20,
                 from mauveAligner.cpp:22:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void 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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: 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
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize    -Wl,-z,relro -Wl,-z,now -o mauveAligner mauveAligner.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scoreAlignment.o scoreAlignment.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<long long unsigned int, long long unsigned int>&}; _Tp = std::pair<long long unsigned int, long long unsigned int>; _Alloc = std::allocator<std::pair<long long unsigned int, long long unsigned int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, long long unsigned int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, long long unsigned int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'virtual void VectorIntervalMap::add(gnSeqI, gnSeqI)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/MatchList.h:22,
                 from scoreAlignment.cpp:13:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Match.h:20,
                 from /usr/include/libMems/MatchList.h:22,
                 from scoreAlignment.cpp:13:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/MatchList.h:18,
                 from scoreAlignment.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqueMerCount.o uniqueMerCount.cpp
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toRawSequence.o toRawSequence.cpp
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mfa2xmfa.o mfa2xmfa.cpp
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mfa2xmfa mfa2xmfa.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o addUnalignedIntervals.o addUnalignedIntervals.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from addUnalignedIntervals.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from addUnalignedIntervals.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from addUnalignedIntervals.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o addUnalignedIntervals addUnalignedIntervals.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toMultiFastA.o toMultiFastA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from toMultiFastA.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from toMultiFastA.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void 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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: 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
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from toMultiFastA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getAlignmentWindows.o getAlignmentWindows.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from getAlignmentWindows.cpp:14:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from getAlignmentWindows.cpp:13:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from getAlignmentWindows.cpp:13:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from getAlignmentWindows.cpp:13:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getAlignmentWindows getAlignmentWindows.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniquifyTrees.o uniquifyTrees.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from uniquifyTrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator<TreeNode>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<TreeNode, std::allocator<TreeNode> >::iterator' {aka '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from uniquifyTrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniquifyTrees uniquifyTrees.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toGrimmFormat.o toGrimmFormat.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from toGrimmFormat.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from toGrimmFormat.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void 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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: 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
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from toGrimmFormat.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toGrimmFormat toGrimmFormat.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from mauveToXMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from mauveToXMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from mauveToXMFA.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from mauveToXMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from mauveToXMFA.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from mauveToXMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void 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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: 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
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from mauveToXMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mauveToXMFA mauveToXMFA.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripGapColumns.o stripGapColumns.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from stripGapColumns.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from stripGapColumns.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from stripGapColumns.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from stripGapColumns.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from stripGapColumns.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from stripGapColumns.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from stripGapColumns.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripGapColumns stripGapColumns.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from progressiveMauve.cpp:26:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
progressiveMauve.cpp:417:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl;
                                                    ^~~~~~~~
progressiveMauve.cpp:417:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
   cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl;
                                                                          ^~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/MatchFinder.h:17,
                 from /usr/include/libMems/MemHash.h:20,
                 from progressiveMauve.cpp:21:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void applyBackbone(mems::IntervalList&, std::__cxx11::string&, std::__cxx11::string&, size_t, double, double, double)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Match.h:20,
                 from /usr/include/libMems/MatchFinder.h:17,
                 from /usr/include/libMems/MemHash.h:20,
                 from progressiveMauve.cpp:21:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UniqueMatchFinder.o UniqueMatchFinder.cpp
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator<TreeNode>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<TreeNode, std::allocator<TreeNode> >::iterator' {aka '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>&}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; _Distance = int; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
       std::__make_heap(__first, __middle, __comp);
       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o createBackboneMFA.o createBackboneMFA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from createBackboneMFA.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from createBackboneMFA.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void 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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: 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
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from createBackboneMFA.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o repeatoire.o repeatoire.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from repeatoire.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from repeatoire.cpp:2:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GappedMatchRecord&}; _Tp = GappedMatchRecord; _Alloc = std::allocator<GappedMatchRecord>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> >::iterator' {aka '__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> >::iterator' {aka '__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, UngappedMatchRecord*>}; _Tp = std::pair<long long int, UngappedMatchRecord*>; _Alloc = std::allocator<std::pair<long long int, UngappedMatchRecord*> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, UngappedMatchRecord*> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'void writeXmfa(mems::MatchList&, std::vector<GappedMatchRecord*>&, const string&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'void writeXML(mems::MatchList&, std::vector<GappedMatchRecord*>&, const string&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >; _Distance = int; _Tp = std::pair<long long int, UngappedMatchRecord*>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __comp);
       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __comp);
       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval<GappedBaseImpl>::GetColumnAndMatch(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment<MatchRecord>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from repeatoire.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, UngappedMatchRecord*>*, std::vector<std::pair<long long int, UngappedMatchRecord*> > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> >*, std::vector<std::pair<long long unsigned int, std::pair<MatchRecord*, unsigned int> > > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE    
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from /usr/include/libMems/ProgressiveAligner.h:21,
                 from alignmentProjector.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from alignmentProjector.cpp:11:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from alignmentProjector.cpp:11:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator<mems::LCB>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::LCB>::iterator' {aka '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: 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
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: 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 file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBLeftComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<mems::LCBIDComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: 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/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBLeftComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<mems::LCBIDComparator>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector<MatchPtrType>&, std::vector<double>&, std::vector<mems::LCB>&) [with MatchVector = std::vector<mems::MatchProjectionAdapter*>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/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*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: 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
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: 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
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<mems::MatchProjectionAdapter*>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: 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
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: 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
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: 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
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int, std::allocator<unsigned int> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>&}; _Tp = boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> >; _Alloc = std::allocator<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> > >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> >*, std::vector<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> > > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from stripSubsetLCBs.cpp:12:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from stripSubsetLCBs.cpp:12:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> >*, std::vector<boost::tuples::tuple<unsigned int, long long unsigned int, long long unsigned int, std::vector<unsigned int> > > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from projectAndStrip.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from projectAndStrip.cpp:12:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from projectAndStrip.cpp:12:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: 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
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: 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 file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/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*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: 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
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: 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/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: 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
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector<long long unsigned int>&) [with MatchVector = std::vector<mems::GappedAlignment*>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: 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
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: 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
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: 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
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from makeBadgerMatrix.cpp:10:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from makeBadgerMatrix.cpp:10:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from randomGeneSample.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from randomGeneSample.cpp:12:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector<std::vector<std::pair<long long int, long long int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from randomGeneSample.cpp:12:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from getOrthologList.cpp:18:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from getOrthologList.cpp:12:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long unsigned int, unsigned int>}; _Tp = std::pair<long long unsigned int, unsigned int>; _Alloc = std::allocator<std::pair<long long unsigned int, unsigned int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, unsigned int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector<std::vector<std::pair<long long int, long long int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from getOrthologList.cpp:12:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >; _Distance = int; _Tp = std::pair<long long unsigned int, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __comp);
       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, unsigned int>*, std::vector<std::pair<long long unsigned int, unsigned int> > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from /usr/include/libMems/Backbone.h:24,
                 from bbFilter.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbFilter.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector<std::vector<std::pair<long long int, long long int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from /usr/include/libMems/Backbone.h:24,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<2, std::allocator<long long int>, std::allocator<unsigned int> > > >}; _Tp = std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > >; _Alloc = std::allocator<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > > >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > >*, std::vector<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > > > >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {genome::gnLocation}; _Tp = genome::gnLocation; _Alloc = std::allocator<genome::gnLocation>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<genome::gnLocation>::iterator' {aka '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<genome::gnLocation>::iterator' {aka '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector<std::vector<std::pair<long long int, long long int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneColsFile(std::istream&, std::vector<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > >*, std::vector<std::pair<unsigned int, mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> > > > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator<TreeNode>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<TreeNode, std::allocator<TreeNode> >::iterator' {aka '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = TreeNode; _Alloc = std::allocator<TreeNode>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>}; _Tp = boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >; _Alloc = std::allocator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > >::iterator' {aka '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/set:60,
                 from /usr/include/libMems/Match.h:18,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<AnalRowComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AnalRowComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<LocComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >; _Distance = int; _Tp = boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AnalRowComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AnalRowComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AnalRowComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
       std::__make_heap(__first, __middle, __comp);
       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mfAnalyze(std::ofstream&, multifun_map_t&, multifun_map_t&, multifun_names_t&, double)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> >*, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double, double, std::__cxx11::basic_string<char> > > >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >; _Distance = int; _Tp = genome::gnLocation; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocComp>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
       std::__make_heap(__first, __middle, __comp);
       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void identifyIntergenicRanges(std::vector<genome::gnSequence*>&, std::vector<std::vector<std::pair<unsigned int, unsigned int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/algorithm:62,
                 from /usr/include/libMems/AbstractMatch.h:18,
                 from /usr/include/libMems/SparseAbstractMatch.h:18,
                 from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/map:61,
                 from /usr/include/libMems/MemHash.h:17,
                 from /usr/include/libMems/IntervalList.h:23,
                 from /usr/include/libMems/Backbone.h:18,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_map.h: In function 'void makeMultiFunCount(genome::gnSequence*, multifun_map_t&, multifun_names_t&, mems::bitset_t&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/Backbone.h:16,
                 from bbAnalyze.cpp:4:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from /usr/include/libMems/Backbone.h:24,
                 from backbone_global_to_local.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from backbone_global_to_local.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long int, long long int>}; _Tp = std::pair<long long int, long long int>; _Alloc = std::allocator<std::pair<long long int, long long int> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<long long int, long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >'} changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector<std::vector<std::pair<long long int, long long int> > >&)':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long int, long long int>*, std::vector<std::pair<long long int, long long int> > >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from backbone_global_to_local.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from backbone_global_to_local.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/ext/hash_map:60,
                 from /usr/include/libMems/HomologyHMM/dptables.h:43,
                 from /usr/include/libMems/HomologyHMM/homology.h:27,
                 from /usr/include/libMems/Islands.h:25,
                 from /usr/include/libMems/ProgressiveAligner.h:21,
                 from xmfa2maf.cpp:2:
/usr/arm-linux-gnueabi/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from xmfa2maf.cpp:1:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from xmfa2maf.cpp:1:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from xmfa2maf.cpp:1:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE    -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function '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>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/libMems/Match.h:22,
                 from /usr/include/libMems/Interval.h:21,
                 from /usr/include/libMems/IntervalList.h:22,
                 from coordinateTranslate.cpp:5:
/usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/include/libMems/Interval.h:18,
                 from /usr/include/libMems/IntervalList.h:22,
                 from coordinateTranslate.cpp:5:
/usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch<gnSeqIAlloc, uintAlloc>::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator<long long unsigned int>; uintAlloc = std::allocator<unsigned int>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1318:58: 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
       { return _M_erase(begin() + (__position - cbegin())); }
                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:69,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval<mems::AbstractGappedAlignment<mems::SparseAbstractMatch<std::allocator<long long unsigned int>, std::allocator<unsigned int> > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator<mems::GenericInterval<> >]':
/usr/arm-linux-gnueabi/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > >::iterator' {aka '__gnu_cxx::__normal_iterator<mems::GenericInterval<>*, std::vector<mems::GenericInterval<>, std::allocator<mems::GenericInterval<> > > >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/8/vector:64,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from /usr/include/libMems/SortedMerList.h:19,
                 from /usr/include/libMems/IntervalList.h:20,
                 from coordinateTranslate.cpp:5:
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]':
/usr/arm-linux-gnueabi/include/c++/8/bits/stl_vector.h:1085:4: 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
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -L/usr/lib/arm-linux-gnueabi -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE   
make[3]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
   dh_auto_test -a
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch
   dh_testroot -a
   dh_prep -a
   dh_auto_install -a
	make -j1 install DESTDIR=/<<BUILDDIR>>/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
 /bin/mkdir -p '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin'
  /usr/bin/install -c mauveAligner scoreAlignment uniqueMerCount toRawSequence mfa2xmfa addUnalignedIntervals toMultiFastA getAlignmentWindows uniquifyTrees toGrimmFormat mauveToXMFA stripGapColumns progressiveMauve extractBCITrees createBackboneMFA repeatoire alignmentProjector stripSubsetLCBs projectAndStrip makeBadgerMatrix randomGeneSample getOrthologList bbFilter bbAnalyze backbone_global_to_local xmfa2maf coordinateTranslate '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg'
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/scoreAlignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/addUnalignedIntervals contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/stripGapColumns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/getOrthologList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toGrimmFormat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/makeBadgerMatrix contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toRawSequence contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/extractBCITrees contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/alignmentProjector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/createBackboneMFA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/getAlignmentWindows contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mfa2xmfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/repeatoire contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/stripSubsetLCBs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mauveToXMFA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toMultiFastA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/xmfa2maf contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/coordinateTranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/backbone_global_to_local contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/projectAndStrip contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mauveAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/bbFilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/uniqueMerCount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/progressiveMauve contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/bbAnalyze contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/randomGeneSample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/uniquifyTrees contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/uniquifyTrees were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/uniquifyTrees were not linked against libboost_system.so.1.67.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/uniquifyTrees were not linked against libMUSCLE.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/uniquifyTrees were not linked against libpthread.so.0 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-4_armel.deb'.
dpkg-deb: building package 'progressivemauve-dbgsym' in '../progressivemauve-dbgsym_1.2.0+4713+dfsg-4_armel.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any >../progressivemauve_1.2.0+4713+dfsg-4_armel.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-06-11T20:51:37Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


lintian
-------


Setup apt archive
-----------------

Merged Build-Depends: lintian:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<BUILDDIR>>/resolver-NGQHVR/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-progressivemauve-dummy
dpkg-scanpackages: info: Wrote 4 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release [963 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Sources [822 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ Packages [897 B]
Fetched 2682 B in 0s (139 kB/s)
Reading package lists...
Reading package lists...

Install lintian build dependencies (apt-based resolver)
-------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl
  libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl
  libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl
  libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl
  libio-pty-perl libio-socket-ssl-perl libipc-run-perl
  libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl
  libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
  libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl
  libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl
  libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl
  libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils
  perl-openssl-defaults readline-common t1utils
Suggested packages:
  libdata-dump-perl ca-certificates libhtml-template-perl libwww-perl
  binutils-multiarch libtext-template-perl readline-doc
Recommended packages:
  gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl
  libsereal-perl libtest-fatal-perl libtest-refcount-perl
  libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl
  libauthen-sasl-perl libunicode-utf8-perl libperlio-gzip-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl
  libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl
  libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl
  libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl
  libio-pty-perl libio-socket-ssl-perl libipc-run-perl
  libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl
  libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
  libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl
  libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl
  libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl
  libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils
  perl-openssl-defaults readline-common
  sbuild-build-depends-lintian-dummy:armel t1utils
0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 7774 kB of archives.
After this operation, 20.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NGQHVR/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 7.0-5 [70.6 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline7 amd64 7.0-5 [151 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.13-2 [512 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-3 [641 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-2 [866 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.15.0 [1181 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 7774 kB in 0s (40.1 MB/s)
Selecting previously unselected package netbase.
(Reading database ... 32759 files and directories currently installed.)
Preparing to unpack .../00-netbase_5.6_all.deb ...
Unpacking netbase (5.6) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../01-readline-common_7.0-5_all.deb ...
Unpacking readline-common (7.0-5) ...
Selecting previously unselected package diffstat.
Preparing to unpack .../02-diffstat_1.62-1_amd64.deb ...
Unpacking diffstat (1.62-1) ...
Selecting previously unselected package libassuan0:amd64.
Preparing to unpack .../03-libassuan0_2.5.2-1_amd64.deb ...
Unpacking libassuan0:amd64 (2.5.2-1) ...
Selecting previously unselected package libreadline7:amd64.
Preparing to unpack .../04-libreadline7_7.0-5_amd64.deb ...
Unpacking libreadline7:amd64 (7.0-5) ...
Selecting previously unselected package gpgconf.
Preparing to unpack .../05-gpgconf_2.2.13-2_amd64.deb ...
Unpacking gpgconf (2.2.13-2) ...
Selecting previously unselected package libsqlite3-0:amd64.
Preparing to unpack .../06-libsqlite3-0_3.27.2-3_amd64.deb ...
Unpacking libsqlite3-0:amd64 (3.27.2-3) ...
Selecting previously unselected package gpg.
Preparing to unpack .../07-gpg_2.2.13-2_amd64.deb ...
Unpacking gpg (2.2.13-2) ...
Selecting previously unselected package libapt-pkg-perl.
Preparing to unpack .../08-libapt-pkg-perl_0.1.34+b1_amd64.deb ...
Unpacking libapt-pkg-perl (0.1.34+b1) ...
Selecting previously unselected package libcapture-tiny-perl.
Preparing to unpack .../09-libcapture-tiny-perl_0.48-1_all.deb ...
Unpacking libcapture-tiny-perl (0.48-1) ...
Selecting previously unselected package libhtml-tagset-perl.
Preparing to unpack .../10-libhtml-tagset-perl_3.20-3_all.deb ...
Unpacking libhtml-tagset-perl (3.20-3) ...
Selecting previously unselected package liburi-perl.
Preparing to unpack .../11-liburi-perl_1.76-1_all.deb ...
Unpacking liburi-perl (1.76-1) ...
Selecting previously unselected package libhtml-parser-perl.
Preparing to unpack .../12-libhtml-parser-perl_3.72-3+b3_amd64.deb ...
Unpacking libhtml-parser-perl (3.72-3+b3) ...
Selecting previously unselected package libcgi-pm-perl.
Preparing to unpack .../13-libcgi-pm-perl_4.40-1_all.deb ...
Unpacking libcgi-pm-perl (4.40-1) ...
Selecting previously unselected package libsub-name-perl.
Preparing to unpack .../14-libsub-name-perl_0.21-1+b3_amd64.deb ...
Unpacking libsub-name-perl (0.21-1+b3) ...
Selecting previously unselected package libclass-accessor-perl.
Preparing to unpack .../15-libclass-accessor-perl_0.51-1_all.deb ...
Unpacking libclass-accessor-perl (0.51-1) ...
Selecting previously unselected package libclone-perl.
Preparing to unpack .../16-libclone-perl_0.41-1+b1_amd64.deb ...
Unpacking libclone-perl (0.41-1+b1) ...
Selecting previously unselected package libdigest-hmac-perl.
Preparing to unpack .../17-libdigest-hmac-perl_1.03+dfsg-2_all.deb ...
Unpacking libdigest-hmac-perl (1.03+dfsg-2) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../18-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package libssl1.1:amd64.
Preparing to unpack .../19-libssl1.1_1.1.1c-1_amd64.deb ...
Unpacking libssl1.1:amd64 (1.1.1c-1) ...
Selecting previously unselected package perl-openssl-defaults:amd64.
Preparing to unpack .../20-perl-openssl-defaults_3_amd64.deb ...
Unpacking perl-openssl-defaults:amd64 (3) ...
Selecting previously unselected package libnet-ssleay-perl.
Preparing to unpack .../21-libnet-ssleay-perl_1.85-2+b1_amd64.deb ...
Unpacking libnet-ssleay-perl (1.85-2+b1) ...
Selecting previously unselected package libio-socket-ssl-perl.
Preparing to unpack .../22-libio-socket-ssl-perl_2.060-3_all.deb ...
Unpacking libio-socket-ssl-perl (2.060-3) ...
Selecting previously unselected package libnet-smtp-ssl-perl.
Preparing to unpack .../23-libnet-smtp-ssl-perl_1.04-1_all.deb ...
Unpacking libnet-smtp-ssl-perl (1.04-1) ...
Selecting previously unselected package libmailtools-perl.
Preparing to unpack .../24-libmailtools-perl_2.18-1_all.deb ...
Unpacking libmailtools-perl (2.18-1) ...
Selecting previously unselected package libnet-ip-perl.
Preparing to unpack .../25-libnet-ip-perl_1.26-2_all.deb ...
Unpacking libnet-ip-perl (1.26-2) ...
Selecting previously unselected package libnet-dns-perl.
Preparing to unpack .../26-libnet-dns-perl_1.19-1_all.deb ...
Unpacking libnet-dns-perl (1.19-1) ...
Selecting previously unselected package libnet-domain-tld-perl.
Preparing to unpack .../27-libnet-domain-tld-perl_1.75-1_all.deb ...
Unpacking libnet-domain-tld-perl (1.75-1) ...
Selecting previously unselected package libemail-valid-perl.
Preparing to unpack .../28-libemail-valid-perl_1.202-1_all.deb ...
Unpacking libemail-valid-perl (1.202-1) ...
Selecting previously unselected package libexporter-tiny-perl.
Preparing to unpack .../29-libexporter-tiny-perl_1.002001-1_all.deb ...
Unpacking libexporter-tiny-perl (1.002001-1) ...
Selecting previously unselected package libipc-system-simple-perl.
Preparing to unpack .../30-libipc-system-simple-perl_1.25-4_all.deb ...
Unpacking libipc-system-simple-perl (1.25-4) ...
Selecting previously unselected package libfile-basedir-perl.
Preparing to unpack .../31-libfile-basedir-perl_0.08-1_all.deb ...
Unpacking libfile-basedir-perl (0.08-1) ...
Selecting previously unselected package libfuture-perl.
Preparing to unpack .../32-libfuture-perl_0.39-1_all.deb ...
Unpacking libfuture-perl (0.39-1) ...
Selecting previously unselected package libstruct-dumb-perl.
Preparing to unpack .../33-libstruct-dumb-perl_0.09-1_all.deb ...
Unpacking libstruct-dumb-perl (0.09-1) ...
Selecting previously unselected package libio-async-perl.
Preparing to unpack .../34-libio-async-perl_0.72-1_all.deb ...
Unpacking libio-async-perl (0.72-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../35-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b5) ...
Selecting previously unselected package libipc-run-perl.
Preparing to unpack .../36-libipc-run-perl_20180523.0-1_all.deb ...
Unpacking libipc-run-perl (20180523.0-1) ...
Selecting previously unselected package liblist-moreutils-perl.
Preparing to unpack .../37-liblist-moreutils-perl_0.416-1+b4_amd64.deb ...
Unpacking liblist-moreutils-perl (0.416-1+b4) ...
Selecting previously unselected package libparse-debianchangelog-perl.
Preparing to unpack .../38-libparse-debianchangelog-perl_1.2.0-13_all.deb ...
Unpacking libparse-debianchangelog-perl (1.2.0-13) ...
Selecting previously unselected package libpath-tiny-perl.
Preparing to unpack .../39-libpath-tiny-perl_0.108-1_all.deb ...
Unpacking libpath-tiny-perl (0.108-1) ...
Selecting previously unselected package libtext-levenshtein-perl.
Preparing to unpack .../40-libtext-levenshtein-perl_0.13-1_all.deb ...
Unpacking libtext-levenshtein-perl (0.13-1) ...
Selecting previously unselected package libtry-tiny-perl.
Preparing to unpack .../41-libtry-tiny-perl_0.30-1_all.deb ...
Unpacking libtry-tiny-perl (0.30-1) ...
Selecting previously unselected package libyaml-0-2:amd64.
Preparing to unpack .../42-libyaml-0-2_0.2.1-1_amd64.deb ...
Unpacking libyaml-0-2:amd64 (0.2.1-1) ...
Selecting previously unselected package libyaml-libyaml-perl.
Preparing to unpack .../43-libyaml-libyaml-perl_0.76+repack-1_amd64.deb ...
Unpacking libyaml-libyaml-perl (0.76+repack-1) ...
Selecting previously unselected package patchutils.
Preparing to unpack .../44-patchutils_0.3.4-2_amd64.deb ...
Unpacking patchutils (0.3.4-2) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../45-t1utils_1.41-3_amd64.deb ...
Unpacking t1utils (1.41-3) ...
Selecting previously unselected package lintian.
Preparing to unpack .../46-lintian_2.15.0_all.deb ...
Unpacking lintian (2.15.0) ...
Selecting previously unselected package sbuild-build-depends-lintian-dummy:armel.
Preparing to unpack .../47-sbuild-build-depends-lintian-dummy_0.invalid.0_armel.deb ...
Unpacking sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ...
Setting up libapt-pkg-perl (0.1.34+b1) ...
Setting up libstruct-dumb-perl (0.09-1) ...
Setting up libio-pty-perl (1:1.08-1.1+b5) ...
Setting up libclone-perl (0.41-1+b1) ...
Setting up libyaml-0-2:amd64 (0.2.1-1) ...
Setting up libssl1.1:amd64 (1.1.1c-1) ...
Setting up libhtml-tagset-perl (3.20-3) ...
Setting up libsqlite3-0:amd64 (3.27.2-3) ...
Setting up libfuture-perl (0.39-1) ...
Setting up libyaml-libyaml-perl (0.76+repack-1) ...
Setting up libtry-tiny-perl (0.30-1) ...
Setting up perl-openssl-defaults:amd64 (3) ...
Setting up libtext-levenshtein-perl (0.13-1) ...
Setting up libassuan0:amd64 (2.5.2-1) ...
Setting up libio-async-perl (0.72-1) ...
Setting up patchutils (0.3.4-2) ...
Setting up libdigest-hmac-perl (1.03+dfsg-2) ...
Setting up libipc-system-simple-perl (1.25-4) ...
Setting up libnet-domain-tld-perl (1.75-1) ...
Setting up t1utils (1.41-3) ...
Setting up diffstat (1.62-1) ...
Setting up libipc-run-perl (20180523.0-1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsub-name-perl (0.21-1+b3) ...
Setting up libpath-tiny-perl (0.108-1) ...
Setting up netbase (5.6) ...
Setting up libexporter-tiny-perl (1.002001-1) ...
Setting up libclass-accessor-perl (0.51-1) ...
Setting up libnet-ip-perl (1.26-2) ...
Setting up readline-common (7.0-5) ...
Setting up liburi-perl (1.76-1) ...
Setting up libreadline7:amd64 (7.0-5) ...
Setting up libnet-ssleay-perl (1.85-2+b1) ...
Setting up libfile-basedir-perl (0.08-1) ...
Setting up liblist-moreutils-perl (0.416-1+b4) ...
Setting up libnet-dns-perl (1.19-1) ...
Setting up libhtml-parser-perl (3.72-3+b3) ...
Setting up gpgconf (2.2.13-2) ...
Setting up libio-socket-ssl-perl (2.060-3) ...
Setting up gpg (2.2.13-2) ...
Setting up libcgi-pm-perl (4.40-1) ...
Setting up libnet-smtp-ssl-perl (1.04-1) ...
Setting up libmailtools-perl (2.18-1) ...
Setting up libparse-debianchangelog-perl (1.2.0-13) ...
Setting up libemail-valid-perl (1.202-1) ...
Setting up lintian (2.15.0) ...
Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ...
Processing triggers for man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.28-10) ...

I: Lintian run was successful.

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


progressivemauve_1.2.0+4713+dfsg-4_armel.changes:
-------------------------------------------------

Format: 1.8
Date: Tue, 04 Dec 2018 10:03:31 +0100
Source: progressivemauve
Binary: progressivemauve progressivemauve-dbgsym
Built-For-Profiles: cross nocheck
Architecture: armel
Version: 1.2.0+4713+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 progressivemauve - multiple genome alignment algorithms
Closes: 914049
Changes:
 progressivemauve (1.2.0+4713+dfsg-4) unstable; urgency=medium
 .
   [ Giovanni Mascellani ]
   * Fix FTBFS with boost1.67
     Closes: #914049
 .
   [ Andreas Tille ]
   * Standards-Version: 4.2.1
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+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

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Source: progressivemauve
Binary: progressivemauve
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Tue, 11 Jun 2019 20:51:36 +0000
Build-Path: /<<BUILDDIR>>/progressivemauve-1.2.0+4713+dfsg
Installed-Build-Depends:
 autoconf (= 2.69-11),
 automake (= 1:1.16.1-4),
 autopoint (= 0.19.8.1-9),
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 libgenome-dev (= 1.3.11+svn20110227.4616-2),
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 libicu-dev (= 63.2-2),
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Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_US.UTF-8"
 LC_ALL="POSIX"
 SOURCE_DATE_EPOCH="1543914211"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


progressivemauve-dbgsym_1.2.0+4713+dfsg-4_armel.deb
---------------------------------------------------

 new Debian package, version 2.0.
 size 16897616 bytes: control archive=1792 bytes.
    1494 bytes,    12 lines      control              
    2862 bytes,    27 lines      md5sums              
 Package: progressivemauve-dbgsym
 Source: progressivemauve
 Version: 1.2.0+4713+dfsg-4
 Auto-Built-Package: debug-symbols
 Architecture: armel
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 17641
 Depends: progressivemauve (= 1.2.0+4713+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for progressivemauve
 Build-Ids: 058920e511ec1a8e088a84732c44cc0a4ec1145e 07279835369da9dfed7975e73c8ef0c507d97e13 1645a9c1439bbbc119ad0cfcdc870ddc62df767c 1ac6c9158bf3f3e9143c64901f10465699a17b16 2a8d973c1119011f0b4dc4eec6d551c7f755688d 427712b03819efc160f3c2eea4df4238e148eba5 4c2a709f3f79021e28b537af1b5e59e4164446cc 5077d38127c3038c51340ad3590321aba449ce07 5176b3ee99a01d7317fc3b3f9224860af4066364 5e1a459feb21855db05566d567d4066c32d5f9b2 634cee3c85f524282222f8980cb0c7bf2e416e80 79593793574ae8edb41afa57de3545463a6580fb 7d1add854dc2459057d2d094d9aca9ad7d7a7519 7d44cba98fa3d061f2743243eacf2485c4d066d1 823a8879f28a85382aeff9170bee9d7bc5020900 9647c5f489e7b233e37f2ac1f67ce0425ddff093 a5adc8d30a5b6cbed8e68ecb03bbf5f842aaa22c af45d2d82a4b8e2c69a0d65c5d60d2d531876ef3 af690d6f91f36a6ec93225f4d2250f12598ade53 b4136e8e4d5025fc4dee9a6d0714caa5ba1599d3 b765d23b99e103da7a8665ec51f763c742e66b87 c09c89e516a88e6ff1c372ca1ec21f26017794b1 c89804a9d8824bf1856a0a223ef474592f2c43fd d578d38589fae00b3682a8c9a84e8bbfa359bdc1 d7eca71c76c0e75f6484c0fa28a9689917d969b3 dd062e36efccd496b234b2a8ab3fa5f5a83a1a2b f5051c8368ee17aeb1b32d7d2aa082921f48ca19

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drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/doc/
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/doc/progressivemauve-dbgsym -> progressivemauve


progressivemauve_1.2.0+4713+dfsg-4_armel.deb
--------------------------------------------

 new Debian package, version 2.0.
 size 646608 bytes: control archive=2496 bytes.
    1927 bytes,    36 lines      control              
    2744 bytes,    42 lines      md5sums              
 Package: progressivemauve
 Version: 1.2.0+4713+dfsg-4
 Architecture: armel
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3683
 Depends: libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgenome0, libmems1, libmuscle1 (>= 3.7+4565), libstdc++6 (>= 5.2)
 Enhances: mauve-aligner
 Section: science
 Priority: optional
 Homepage: http://darlinglab.org/mauve/user-guide/mauvealigner.html
 Description: multiple genome alignment algorithms
  The mauveAligner and progressiveMauve alignment algorithms have been
  implemented as command-line programs included with the downloadable Mauve
  software.  When run from the command-line, these programs provide options
  not yet available in the graphical interface.
  .
  Mauve is a system for efficiently constructing multiple genome alignments
  in the presence of large-scale evolutionary events such as rearrangement
  and inversion. Multiple genome alignment provides a basis for research
  into comparative genomics and the study of evolutionary dynamics.  Aligning
  whole genomes is a fundamentally different problem than aligning short
  sequences.
  .
  Mauve has been developed with the idea that a multiple genome aligner
  should require only modest computational resources. It employs algorithmic
  techniques that scale well in the amount of sequence being aligned. For
  example, a pair of Y. pestis genomes can be aligned in under a minute,
  while a group of 9 divergent Enterobacterial genomes can be aligned in
  a few hours.
  .
  Mauve computes and interactively visualizes genome sequence comparisons.
  Using FastA or GenBank sequence data, Mauve constructs multiple genome
  alignments that identify large-scale rearrangement, gene gain, gene loss,
  indels, and nucleotide substutition.
  .
  Mauve is developed at the University of Wisconsin.

drwxr-xr-x root/root         0 2018-12-04 09:03 ./
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/bin/
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/addUnalignedIntervals
-rwxr-xr-x root/root    181764 2018-12-04 09:03 ./usr/bin/alignmentProjector
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/backbone_global_to_local
-rwxr-xr-x root/root    308756 2018-12-04 09:03 ./usr/bin/bbAnalyze
-rwxr-xr-x root/root     50640 2018-12-04 09:03 ./usr/bin/bbFilter
-rwxr-xr-x root/root    112132 2018-12-04 09:03 ./usr/bin/coordinateTranslate
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/createBackboneMFA
-rwxr-xr-x root/root     79312 2018-12-04 09:03 ./usr/bin/extractBCITrees
-rwxr-xr-x root/root    140804 2018-12-04 09:03 ./usr/bin/getAlignmentWindows
-rwxr-xr-x root/root    185860 2018-12-04 09:03 ./usr/bin/getOrthologList
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/makeBadgerMatrix
-rwxr-xr-x root/root    183292 2018-12-04 09:03 ./usr/bin/mauveAligner
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/mauveToXMFA
-rwxr-xr-x root/root     17924 2018-12-04 09:03 ./usr/bin/mfa2xmfa
-rwxr-xr-x root/root    269308 2018-12-04 09:03 ./usr/bin/progressiveMauve
-rwxr-xr-x root/root    153092 2018-12-04 09:03 ./usr/bin/projectAndStrip
-rwxr-xr-x root/root    161284 2018-12-04 09:03 ./usr/bin/randomGeneSample
-rwxr-xr-x root/root    474148 2018-12-04 09:03 ./usr/bin/repeatoire
-rwxr-xr-x root/root    124420 2018-12-04 09:03 ./usr/bin/scoreAlignment
-rwxr-xr-x root/root    120324 2018-12-04 09:03 ./usr/bin/stripGapColumns
-rwxr-xr-x root/root    124420 2018-12-04 09:03 ./usr/bin/stripSubsetLCBs
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/toGrimmFormat
-rwxr-xr-x root/root    116228 2018-12-04 09:03 ./usr/bin/toMultiFastA
-rwxr-xr-x root/root      9732 2018-12-04 09:03 ./usr/bin/toRawSequence
-rwxr-xr-x root/root      9732 2018-12-04 09:03 ./usr/bin/uniqueMerCount
-rwxr-xr-x root/root     58832 2018-12-04 09:03 ./usr/bin/uniquifyTrees
-rwxr-xr-x root/root    120324 2018-12-04 09:03 ./usr/bin/xmfa2maf
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/doc/
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/doc/progressivemauve/
-rw-r--r-- root/root       261 2018-12-04 09:03 ./usr/share/doc/progressivemauve/README.test
-rw-r--r-- root/root       818 2018-12-04 09:03 ./usr/share/doc/progressivemauve/changelog.Debian.gz
-rw-r--r-- root/root       776 2018-12-04 09:03 ./usr/share/doc/progressivemauve/copyright
-rw-r--r-- root/root      1244 2018-12-04 09:03 ./usr/share/doc/progressivemauve/run-unit-test
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/
-rw-r--r-- root/root      2203 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/all_virii.fasta.gz
-rw-r--r-- root/root      2848 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_1.gbk.gz
-rw-r--r-- root/root      2879 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_2.gbk.gz
-rw-r--r-- root/root      2878 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_3.gbk.gz
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/man/
drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/share/man/man1/
-rw-r--r-- root/root      1122 2018-12-04 09:03 ./usr/share/man/man1/addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/alignmentProjector.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/backbone_global_to_local.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/bbAnalyze.1.gz -> addUnalignedIntervals.1.gz
-rw-r--r-- root/root       515 2018-12-04 09:03 ./usr/share/man/man1/bbFilter.1.gz
-rw-r--r-- root/root       373 2018-12-04 09:03 ./usr/share/man/man1/coordinateTranslate.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/createBackboneMFA.1.gz -> addUnalignedIntervals.1.gz
-rw-r--r-- root/root       525 2018-12-04 09:03 ./usr/share/man/man1/extractBCITrees.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/getAlignmentWindows.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/getOrthologList.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/makeBadgerMatrix.1.gz -> addUnalignedIntervals.1.gz
-rw-r--r-- root/root      1516 2018-12-04 09:03 ./usr/share/man/man1/mauveAligner.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/mauveToXMFA.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/mfa2xmfa.1.gz -> addUnalignedIntervals.1.gz
-rw-r--r-- root/root      1987 2018-12-04 09:03 ./usr/share/man/man1/progressiveMauve.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/projectAndStrip.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/randomGeneSample.1.gz -> addUnalignedIntervals.1.gz
-rw-r--r-- root/root       919 2018-12-04 09:03 ./usr/share/man/man1/repeatoire.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/scoreAlignment.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/stripGapColumns.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/stripSubsetLCBs.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/toGrimmFormat.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/toMultiFastA.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/toRawSequence.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/uniqueMerCount.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/uniquifyTrees.1.gz -> addUnalignedIntervals.1.gz
lrwxrwxrwx root/root         0 2018-12-04 09:03 ./usr/share/man/man1/xmfa2maf.1.gz -> addUnalignedIntervals.1.gz


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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 194056
Build-Time: 327
Distribution: unstable
Foreign Architectures: armel
Host Architecture: armel
Install-Time: 31
Job: progressivemauve_1.2.0+4713+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: progressivemauve
Package-Time: 368
Source-Version: 1.2.0+4713+dfsg-4
Space: 194056
Status: successful
Version: 1.2.0+4713+dfsg-4
--------------------------------------------------------------------------------
Finished at 2019-06-11T20:51:37Z
Build needed 00:06:08, 194056k disk space