sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org

+==============================================================================+
| progressivemauve 1.2.0+4713+dfsg-4 (armel)   Thu, 27 Feb 2020 22:05:58 +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-25cd0d3d-4bf2-4ebb-b604-dfbca4390d3c' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/progressivemauve-vtmrQg/resolver-IIDc9C' with '<<RESOLVERDIR>>'

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

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 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 2020-02-27-0814.40.pdiff [5599 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-27-1419.01.pdiff [20.1 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-27-2017.46.pdiff [11.9 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-27-2017.46.pdiff [11.9 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-27-0814.40.pdiff [4633 B]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-27-1419.01.pdiff [24.4 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-27-2017.46.pdiff [11.6 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-27-2017.46.pdiff [11.6 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main armel Packages [7941 kB]
Fetched 8217 kB in 2s (4852 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


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 (3923 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/progressivemauve-vtmrQg/progressivemauve-1.2.0+4713+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/progressivemauve-vtmrQg' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel
Filtered Build-Depends: debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [455 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [545 B]
Fetched 1957 B in 0s (99.3 kB/s)
Reading package lists...
Reading package lists...

Install main 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 binutils-arm-linux-gnueabi
  bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9
  g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel
  gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base
  gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base
  groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armel
  libasan5-armel-cross libatomic1:armel libatomic1-armel-cross
  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-armel-cross libc6-dev libc6-dev:armel
  libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3
  libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel
  libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross
  libgenome-dev:armel libgenome0:armel libglib2.0-0 libgomp1:armel
  libgomp1-armel-cross libicu-dev:armel libicu63 libicu63:armel
  libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libmems-dev:armel libmems1:armel libmuscle-dev:armel libmuscle1:armel
  libpipeline1 libpkgconf3 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armel
  libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db pkgconf po-debconf
  sensible-utils ucf zlib1g:armel
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
  | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch
  g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison
  gdb-arm-linux-gnueabi gcc-doc 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-contract1.67-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 glibc-doc manpages-dev:armel icu-doc:armel libstdc++-9-doc
  libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk
  libyaml-shell-perl 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 libltdl-dev libwww-perl libxml-sax-expat-perl
  libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi
  bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9
  g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel
  gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base
  gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base
  groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armel
  libasan5-armel-cross libatomic1:armel libatomic1-armel-cross
  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-armel-cross libc6-dev libc6-dev:armel
  libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3
  libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel
  libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross
  libgenome-dev:armel libgenome0:armel libglib2.0-0 libgomp1:armel
  libgomp1-armel-cross libicu-dev:armel libicu63 libicu63:armel
  libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libmems-dev:armel libmems1:armel libmuscle-dev:armel libmuscle1:armel
  libpipeline1 libpkgconf3 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armel
  libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db pkgconf po-debconf
  sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel
0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded.
Need to get 108 MB of archives.
After this operation, 554 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 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 1.22.4-4 [919 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10-20200222-1 [195 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-30 [196 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-3 [2745 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.10-10 [104 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-10 [2638 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-28cross1 [195 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [6813 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-28cross1 [191 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200211-1cross1 [191 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-9cross1 [1128 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200211-1cross1 [38.3 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200211-1cross1 [85.0 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200211-1cross1 [8668 B]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-28cross1 [340 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200211-1cross1 [369 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200211-1cross1 [114 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-28cross1 [643 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7165 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.8-1cross1 [1128 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-9cross1 [2141 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-28cross1 [1710 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7394 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-4 [709 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-13 [513 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.5-1 [1320 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 icu-devtools amd64 63.2-2 [189 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10-20200222-1 [38.3 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.10-10 [100 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-10 [2338 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-30 [347 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10-20200222-1 [8852 B]
Get:88 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10-20200222-1 [86.8 kB]
Get:89 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10-20200222-1 [408 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10-20200222-1 [115 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-30 [645 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.4.19-1 [1057 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.10-10 [120 kB]
Get:94 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-10 [2184 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-30 [1741 kB]
Get:96 http://debian.oregonstate.edu/debian unstable/main armel libboost1.67-dev armel 1.67.0-17 [8389 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main armel libboost-dev armel 1.67.0.2+b1 [4488 B]
Get:98 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67.0 armel 1.67.0-17 [230 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67.0 armel 1.67.0-17 [255 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67-dev armel 1.67.0-17 [232 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67-dev armel 1.67.0-17 [264 kB]
Get:102 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem-dev armel 1.67.0.2+b1 [4304 B]
Get:103 http://debian.oregonstate.edu/debian unstable/main armel libicu63 armel 63.2-2 [7979 kB]
Get:104 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67.0 armel 1.67.0-17 [454 kB]
Get:105 http://debian.oregonstate.edu/debian unstable/main armel libicu-dev armel 63.2-2 [8922 kB]
Get:106 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67-dev armel 1.67.0-17 [556 kB]
Get:107 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-2 [45.3 kB]
Get:108 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB]
Get:109 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67.0 armel 1.67.0-17 [246 kB]
Get:110 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67-dev armel 1.67.0-17 [256 kB]
Get:111 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams-dev armel 1.67.0.2+b1 [4252 B]
Get:112 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67.0 armel 1.67.0-17 [332 kB]
Get:113 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67-dev armel 1.67.0-17 [383 kB]
Get:114 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options-dev armel 1.67.0.2+b1 [4284 B]
Get:115 http://debian.oregonstate.edu/debian unstable/main armel libboost-system-dev armel 1.67.0.2+b1 [4404 B]
Get:116 http://debian.oregonstate.edu/debian unstable/main armel libgenome0 armel 1.3.11+svn20110227.4616-2 [96.5 kB]
Get:117 http://debian.oregonstate.edu/debian unstable/main armel libgenome-dev armel 1.3.11+svn20110227.4616-2 [173 kB]
Get:118 http://debian.oregonstate.edu/debian unstable/main armel libmuscle1 armel 3.7+4565-6 [200 kB]
Get:119 http://debian.oregonstate.edu/debian unstable/main armel libmems1 armel 1.6.0+4725-8+b1 [525 kB]
Get:120 http://debian.oregonstate.edu/debian unstable/main armel libmuscle-dev armel 3.7+4565-6 [256 kB]
Get:121 http://debian.oregonstate.edu/debian unstable/main armel libmems-dev armel 1.6.0+4725-8+b1 [822 kB]
Get:122 http://debian.oregonstate.edu/debian unstable/main amd64 libpkgconf3 amd64 1.6.3-5 [34.8 kB]
Get:123 http://debian.oregonstate.edu/debian unstable/main amd64 pkgconf amd64 1.6.3-5 [40.6 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libgenome0:armel (1.3.11+svn20110227.4616-2) ...
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Setting up libboost-filesystem1.67.0:armel (1.67.0-17) ...
Setting up libstdc++-9-dev:armel (9.2.1-30) ...
Setting up libmems1:armel (1.6.0+4725-8+b1) ...
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Setting up libboost-dev:armel (1.67.0.2+b1) ...
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Setting up libboost-system-dev:armel (1.67.0.2+b1) ...
Setting up libmems-dev:armel (1.6.0+4725-8+b1) ...
Setting up libboost-iostreams-dev:armel (1.67.0.2+b1) ...
Setting up libboost-filesystem-dev:armel (1.67.0.2+b1) ...
Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ...
Processing triggers for libc-bin (2.29-10) ...

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

Arch check ok (armel included in any)

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

Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64)
Toolchain package versions: binutils_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-8_8.3.0-29 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-9-dev_9.2.1-30 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200222-1 libstdc++6-armel-cross_10-20200211-1cross1 linux-libc-dev_5.4.19-1
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-3 binutils-arm-linux-gnueabi_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-29 cpp-9_9.2.1-30 cpp-9-arm-linux-gnueabi_9.2.1-28cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 g++-9-arm-linux-gnueabi_9.2.1-28cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 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libboost-program-options-dev_1.67.0.2+b1 libboost-program-options1.67-dev_1.67.0-17 libboost-program-options1.67.0_1.67.0-17 libboost-regex1.67-dev_1.67.0-17 libboost-regex1.67.0_1.67.0-17 libboost-system-dev_1.67.0.2+b1 libboost-system1.67-dev_1.67.0-17 libboost-system1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-armel-cross_2.29-9cross1 libc6-dev_2.29-10 libc6-dev-armel-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200222-1 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-3 libctf0_2.34-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-3 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-9-dev-armel-cross_9.2.1-28cross1 libgcc-s1_10-20200222-1 libgcc-s1-armel-cross_10-20200211-1cross1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgenome-dev_1.3.11+svn20110227.4616-2 libgenome0_1.3.11+svn20110227.4616-2 libglib2.0-0_2.62.5-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgomp1-armel-cross_10-20200211-1cross1 libgpg-error0_1.37-1 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10-20200222-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200222-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmems-dev_1.6.0+4725-8+b1 libmems1_1.6.0+4725-8+b1 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpkgconf3_1.6.3-5 libquadmath0_10-20200222-1 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.5-2 libstdc++-9-dev_9.2.1-30 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200222-1 libstdc++6-armel-cross_10-20200211-1cross1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libubsan1-armel-cross_10-20200211-1cross1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-4 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 linux-libc-dev-armel-cross_5.4.8-1cross1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 pkgconf_1.6.3-5 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2

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


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

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: progressivemauve
Binary: progressivemauve
Architecture: any
Version: 1.2.0+4713+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://darlinglab.org/mauve/user-guide/mauvealigner.html
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/progressivemauve
Vcs-Git: https://salsa.debian.org/med-team/progressivemauve.git
Testsuite: autopkgtest
Build-Depends: debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev
Package-List:
 progressivemauve deb science optional arch=any
Checksums-Sha1:
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 c360aa1123bf7f17116c87a3916002507ffbb506 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz
Checksums-Sha256:
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 967fc3ede9cabed5d226f680a195cf8381bfe298c66cef6fe307407af99d5daf 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz
Files:
 b9f9a0377aeccaa353cc4a491452003a 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz
 0bd30eeadd7194b9b4c88965367c6cc5 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz

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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 /<<PKGBUILDDIR>>
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=C.UTF-8
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-25cd0d3d-4bf2-4ebb-b604-dfbca4390d3c
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
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 '/<<PKGBUILDDIR>>'
Making all in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make  all-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveAligner.o mauveAligner.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  413 |   cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl;
      |                                                ^~~~~~~~
mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
  413 |   cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl;
      |                                                                      ^~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:171:5: 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from mauveAligner.cpp:18:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scoreAlignment.o scoreAlignment.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘virtual void VectorIntervalMap::add(gnSeqI, gnSeqI)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:171:5: 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o addUnalignedIntervals.o addUnalignedIntervals.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toMultiFastA.o toMultiFastA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getAlignmentWindows.o getAlignmentWindows.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniquifyTrees.o uniquifyTrees.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from uniquifyTrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from uniquifyTrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toGrimmFormat.o toGrimmFormat.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripGapColumns.o stripGapColumns.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
progressiveMauve.cpp:417:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  417 |   cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl;
      |                                                    ^~~~~~~~
progressiveMauve.cpp:417:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
  417 |   cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl;
      |                                                                          ^~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:171:5: 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In function ‘void applyBackbone(mems::IntervalList&, std::string&, std::string&, size_t, double, double, double)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/Matrix.h:19,
                 from progressiveMauve.cpp:17:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1820:5: 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
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  326 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1671:23: 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
 1671 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from extractBCITrees.cpp:4:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libMems/PhyloTree.h:8,
                 from extractBCITrees.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o createBackboneMFA.o createBackboneMFA.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o repeatoire.o repeatoire.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void writeXmfa(mems::MatchList&, std::vector<GappedMatchRecord*>&, const string&)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void writeXML(mems::MatchList&, std::vector<GappedMatchRecord*>&, const string&)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<GappedMatchRecord*, std::vector<GappedMatchRecord, std::allocator<GappedMatchRecord> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
   78 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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++/9/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++/9/bits/stl_algo.h:1820:5: 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
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/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++/9/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
   78 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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++/9/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++/9/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++/9/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++/9/bits/stl_algo.h:1820:5: 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
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1920:34: 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
 1920 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1921 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1920:34: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1920:34: 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
 1920 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1921 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1920:34: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from /usr/include/libGenome/gnGenomeSpec.h:21,
                 from /usr/include/libGenome/gnSequence.h:27,
                 from repeatoire.cpp:1:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: 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
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mems::LCB*, std::vector<mems::LCB> >’ changed in GCC 7.1
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from alignmentProjector.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from alignmentProjector.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from stripSubsetLCBs.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from projectAndStrip.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from projectAndStrip.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from makeBadgerMatrix.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from randomGeneSample.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
   78 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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++/9/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++/9/bits/stl_algo.h:1820:5: 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
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1920:34: 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
 1920 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1921 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1920:34: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 from getOrthologList.cpp:7:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62,
                 from getOrthologList.cpp:8:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/bits/stl_tree.h:2452:7: 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
 2452 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1820:5: 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
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1820 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:1839:5: 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++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void PhyloTree<T>::readTree(std::istream&) [with T = TreeNode]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TreeNode*, std::vector<TreeNode, std::allocator<TreeNode> > >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  326 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: 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
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: 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
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1671:23: 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
 1671 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1967:25: 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
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: 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
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: 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
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
  214 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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
  326 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1939 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1953 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1671 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1967 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1968 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1969 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1884 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genome::gnLocation*, std::vector<genome::gnLocation> >’ changed in GCC 7.1
 1889 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/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++/9/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
  499 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/arm-linux-gnueabi/include/c++/9/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
  499 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:121:4: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/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++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:171:5: 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
  171 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1195 |    _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
  202 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { 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
  195 | }
      | ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/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++/9/bits/stl_vector.h:1428:58: 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
 1428 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                                                          ^
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72,
                 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++/9/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++/9/bits/vector.tcc:426:7: 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
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67,
                 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++/9/bits/stl_vector.h: In member function ‘void mems::GenericIntervalList<MatchType>::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]’:
/usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: 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
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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 '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
 /bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/progressivemauve/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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/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/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/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/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/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/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/uniquifyTrees 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/stripSubsetLCBs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
   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 2020-02-27T22:12:12Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| 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
Architecture: armel
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Thu, 27 Feb 2020 22:12:11 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
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 LANG="en_US.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1543914211"


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


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

 new Debian package, version 2.0.
 size 18348692 bytes: control archive=1784 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: 19096
 Depends: progressivemauve (= 1.2.0+4713+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for progressivemauve
 Build-Ids: 077c1bb175317be0a8ab0a7fc9e5a07fcf477ad7 0df6c719dceb670b928b5122d5affd9993355965 10cb71ba0b04c767ebc89ad1ebcd5dc6646bd412 1354705e17b708ea2e8a0ef2f893d6dc52dc6c64 17486e71b985697205ca9dce695d7a88d4f26fff 193ba8cd22588fb5b99760225c1366b3d81e5a92 1b0cdee6d3e3d087fabe751c2c6e6502eb29f628 1bdcf401cdef45b07833c9259db08014e7db7d73 209ed3d727da6ef414c2be73c6134e8f7501dc4c 3cbaa29367c5458a7ef510076696458f61f4ce6b 3f37e90e265159b6944e03e058c11bee7952556a 3fa64fe8a6e1a7d86b71fd9e3fe51b2303540a32 461ac124a450fad03dd38149d68f6c729a50f52a 5ef11e8d4e056a9ad9568144190aa4046c066f2e 7556e7dd939bd69c1420857ef127edad8f9f0baa 7bb812cad0398c3969a8df9c844269e736795cb5 7f0591a5b363f27d584aca52ddcc04112ba2f228 914cb148f12e47a7c19c34acd69f5f05294920b5 9610f2fa7e507b755ea45d42d4228eddf9f24ec3 975bb6f47d95ef5418648c0e5e7117e4b860748f b40a45e0736d24770203c0fbde640f7c5a3b50cb b8a90a6298e20f68b551bb13928f9f5a88ed7755 c0ba981617d2a6470be52deb754cb7ff9e2885bd e22d84b2c9af477647a14b64c04b12ac7bf01395 e9d6972619c58d7e27b5db66d4c54d9230fd9fd3 f6a4e783fde11841bb100976b0926d525b3fef53 fc70863d758a7a9d822e989f9bb5e2e44a4a83df

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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 661344 bytes: control archive=2484 bytes.
    1877 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: 3991
 Depends: libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-program-options1.67.0, libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgenome0, libmems1, libstdc++6 (>= 9)
 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    128516 2018-12-04 09:03 ./usr/bin/addUnalignedIntervals
-rwxr-xr-x root/root    198148 2018-12-04 09:03 ./usr/bin/alignmentProjector
-rwxr-xr-x root/root    128516 2018-12-04 09:03 ./usr/bin/backbone_global_to_local
-rwxr-xr-x root/root    337428 2018-12-04 09:03 ./usr/bin/bbAnalyze
-rwxr-xr-x root/root     46544 2018-12-04 09:03 ./usr/bin/bbFilter
-rwxr-xr-x root/root    120324 2018-12-04 09:03 ./usr/bin/coordinateTranslate
-rwxr-xr-x root/root    120324 2018-12-04 09:03 ./usr/bin/createBackboneMFA
-rwxr-xr-x root/root     75216 2018-12-04 09:03 ./usr/bin/extractBCITrees
-rwxr-xr-x root/root    157188 2018-12-04 09:03 ./usr/bin/getAlignmentWindows
-rwxr-xr-x root/root    198148 2018-12-04 09:03 ./usr/bin/getOrthologList
-rwxr-xr-x root/root    124420 2018-12-04 09:03 ./usr/bin/makeBadgerMatrix
-rwxr-xr-x root/root    211964 2018-12-04 09:03 ./usr/bin/mauveAligner
-rwxr-xr-x root/root    120324 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    302076 2018-12-04 09:03 ./usr/bin/progressiveMauve
-rwxr-xr-x root/root    165380 2018-12-04 09:03 ./usr/bin/projectAndStrip
-rwxr-xr-x root/root    181764 2018-12-04 09:03 ./usr/bin/randomGeneSample
-rwxr-xr-x root/root    531492 2018-12-04 09:03 ./usr/bin/repeatoire
-rwxr-xr-x root/root    136708 2018-12-04 09:03 ./usr/bin/scoreAlignment
-rwxr-xr-x root/root    132612 2018-12-04 09:03 ./usr/bin/stripGapColumns
-rwxr-xr-x root/root    136708 2018-12-04 09:03 ./usr/bin/stripSubsetLCBs
-rwxr-xr-x root/root    120324 2018-12-04 09:03 ./usr/bin/toGrimmFormat
-rwxr-xr-x root/root    120324 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     54736 2018-12-04 09:03 ./usr/bin/uniquifyTrees
-rwxr-xr-x root/root    128516 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


lintian
-------


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Merged Build-Depends: lintian:amd64
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The following additional packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl
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  libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl
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  libipc-system-simple-perl libjson-perl liblinux-epoll-perl
  liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl
  libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
  libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl
  libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl
  libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl
  libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl
  libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase
  patchutils perl-openssl-defaults readline-common t1utils
Suggested packages:
  libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl
  libbareword-filehandles-perl libindirect-perl libmultidimensional-perl
  libdevel-lexalias-perl libdevel-stacktrace-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 libjson-xs-perl
  libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl
  libnet-libidn-perl libperl4-corelibs-perl libauthen-sasl-perl
  libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl
  libtype-tiny-xs-perl libperlio-gzip-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl
  libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl
  libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl
  libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl
  libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl
  libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl
  libipc-system-simple-perl libjson-perl liblinux-epoll-perl
  liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl
  libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
  libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl
  libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl
  libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl
  libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl
  libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase
  patchutils perl-openssl-defaults readline-common
  sbuild-build-depends-lintian-dummy:armel t1utils
0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded.
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Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.26-1 [27.1 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1 [317 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.43-1 [83.2 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.75-1 [269 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.017-1 [16.8 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.12-1 [36.3 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-perl all 4.02000-2 [88.8 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.008001-2 [331 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.81+repack-1 [35.4 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.55.0 [1312 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libapt-pkg-perl (0.1.36+b2) ...
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Setting up libsub-identify-perl (0.14-1+b2) ...
Setting up libssl1.1:amd64 (1.1.1d-2) ...
Setting up libhtml-tagset-perl (3.20-4) ...
Setting up libdevel-size-perl (0.83-1+b1) ...
Setting up libsqlite3-0:amd64 (3.31.1-3) ...
Setting up libfuture-perl (0.43-1) ...
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Setting up perl-openssl-defaults:amd64 (4) ...
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Setting up libtext-levenshtein-perl (0.13-1) ...
Setting up libassuan0:amd64 (2.5.3-7) ...
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Setting up libio-async-perl (0.75-1) ...
Setting up patchutils (0.3.4-2+b1) ...
Setting up libfile-find-rule-perl (0.34-1) ...
Setting up libdigest-hmac-perl (1.03+dfsg-2) ...
Setting up libipc-system-simple-perl (1.26-1) ...
Setting up libnet-domain-tld-perl (1.75-1) ...
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Setting up diffstat (1.63-1) ...
Setting up libvariable-magic-perl (0.62-1+b2) ...
Setting up libb-hooks-op-check-perl (0.22-1+b2) ...
Setting up libipc-run-perl (20180523.0-2) ...
Setting up libsub-exporter-progressive-perl (0.001013-1) ...
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Setting up libpath-tiny-perl (0.108-1) ...
Setting up libjson-perl (4.02000-2) ...
Setting up librole-tiny-perl (2.001004-1) ...
Setting up netbase (6.1) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006006-1) ...
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Setting up libexporter-tiny-perl (1.002001-1) ...
Setting up libclass-accessor-perl (0.51-1) ...
Setting up libfont-ttf-perl (1.06-1) ...
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Setting up readline-common (8.0-4) ...
Setting up liburi-perl (1.76-2) ...
Setting up libnet-ssleay-perl (1.88-2) ...
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Setting up liblist-moreutils-perl (0.416-1+b5) ...
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Setting up libio-async-loop-epoll-perl (0.20-1) ...
Setting up libhtml-parser-perl (3.72-5) ...
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Setting up gpg (2.2.19-1) ...
Setting up libparams-classify-perl (0.015-1+b2) ...
Setting up libcgi-pm-perl (4.46-1) ...
Setting up libnet-smtp-ssl-perl (1.04-1) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libmailtools-perl (2.21-1) ...
Setting up libmodule-implementation-perl (0.09-1) ...
Setting up libemail-valid-perl (1.202-1) ...
Setting up libpackage-stash-perl (0.38-1) ...
Setting up libimport-into-perl (1.002005-1) ...
Setting up libmoo-perl (2.003006-1) ...
Setting up libmoox-aliases-perl (0.001006-1) ...
Setting up libb-hooks-endofscope-perl (0.24-1) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.55.0) ...
Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ...
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Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.29-10) ...

I: Lintian run was successful.

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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: 214836
Build-Time: 341
Distribution: unstable
Foreign Architectures: armel
Host Architecture: armel
Install-Time: 24
Job: progressivemauve_1.2.0+4713+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: progressivemauve
Package-Time: 374
Source-Version: 1.2.0+4713+dfsg-4
Space: 214836
Status: successful
Version: 1.2.0+4713+dfsg-4
--------------------------------------------------------------------------------
Finished at 2020-02-27T22:12:12Z
Build needed 00:06:14, 214836k disk space