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

+==============================================================================+
| progressivemauve 1.2.0+4713+dfsg-4 (armel)   Tue, 19 Nov 2019 02:08:24 +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-fcdc2269-e63d-40ba-8546-0f7693651fb9' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/progressivemauve-7dIxrq/resolver-xtK6Ji' with '<<RESOLVERDIR>>'

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

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-18-0814.08.pdiff [5773 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-18-1415.12.pdiff [12.2 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-18-2016.45.pdiff [7549 B]
Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-18-2016.45.pdiff [7549 B]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-18-0814.08.pdiff [14.6 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-18-1415.12.pdiff [21.1 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-18-2016.45.pdiff [12.3 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-18-2016.45.pdiff [12.3 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main armel Packages [7930 kB]
Fetched 8198 kB in 2s (4176 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 (2491 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/progressivemauve-7dIxrq/progressivemauve-1.2.0+4713+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/progressivemauve-7dIxrq' 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 [547 B]
Fetched 1959 B in 0s (106 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 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++-9-arm-linux-gnueabi g++-arm-linux-gnueabi
  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:armel libc6-dev-armel-cross
  libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel
  libgcc-9-dev-armel-cross libgcc1:armel libgcc1-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
  libncurses6 libpipeline1 libsigsegv2 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
  gcc-9-doc libstdc++6-9-dbg-armel-cross libgcc1-dbg-armel-cross
  libgomp1-dbg-armel-cross libitm1-dbg-armel-cross libatomic1-dbg-armel-cross
  libasan5-dbg-armel-cross liblsan0-dbg-armel-cross libtsan0-dbg-armel-cross
  libubsan1-dbg-armel-cross libquadmath0-dbg-armel-cross 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-coroutine1.67-dev:armel libboost-date-time1.67-dev:armel
  libboost-exception1.67-dev:armel libboost-fiber1.67-dev:armel
  libboost-graph1.67-dev:armel libboost-graph-parallel1.67-dev:armel
  libboost-locale1.67-dev:armel libboost-log1.67-dev:armel
  libboost-math1.67-dev:armel libboost-mpi1.67-dev:armel
  libboost-mpi-python1.67-dev:armel libboost-numpy1.67-dev:armel
  libboost-python1.67-dev:armel libboost-random1.67-dev:armel
  libboost-serialization1.67-dev:armel libboost-signals1.67-dev:armel
  libboost-stacktrace1.67-dev:armel libboost-test1.67-dev:armel
  libboost-thread1.67-dev:armel libboost-timer1.67-dev:armel
  libboost-type-erasure1.67-dev:armel libboost-wave1.67-dev:armel
  libboost1.67-tools-dev:armel libmpfrc++-dev:armel libntl-dev:armel
  glibc-doc:armel libc-l10n:armel locales:armel manpages-dev:armel
  icu-doc:armel libstdc++-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 libgpm2 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 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++-9-arm-linux-gnueabi g++-arm-linux-gnueabi
  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:armel libc6-dev-armel-cross
  libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel
  libgcc-9-dev-armel-cross libgcc1:armel libgcc1-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
  libncurses6 libpipeline1 libsigsegv2 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, 113 newly installed, 0 to remove and 0 not upgraded.
Need to get 92.8 MB of archives.
After this operation, 485 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 1.22.4-3 [916 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-1 [1307 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-9-base armel 9.2.1-19 [194 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-6 [253 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-6 [119 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-6 [67.2 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.33.1-2 [2721 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-19cross1 [194 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [6812 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-19cross1 [190 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-1cross7 [1139 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armel-cross all 1:9.2.1-19cross1 [39.0 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 9.2.1-19cross1 [74.8 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 9.2.1-19cross1 [8944 B]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-19cross1 [340 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 9.2.1-19cross1 [377 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 9.2.1-19cross1 [110 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-19cross1 [644 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [7157 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.2.9-2cross7 [1312 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-1cross7 [2155 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-19cross1 [1709 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [7390 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b4 [710 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.7.1 [173 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.2-1 [23.6 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.2-1 [14.6 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-2 [145 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.2-3 [1318 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.7.1 [997 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 icu-devtools amd64 63.2-2 [189 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main armel libgcc1 armel 1:9.2.1-19 [38.9 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-3 [2348 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-19 [347 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 9.2.1-19 [9092 B]
Get:80 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 9.2.1-19 [77.1 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 9.2.1-19 [415 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 9.2.1-19 [111 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-19 [643 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.3.9-2 [986 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-3 [2195 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-19 [1739 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main armel libboost1.67-dev armel 1.67.0-13+b1 [8387 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main armel libboost-dev armel 1.67.0.2 [4184 B]
Get:89 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67.0 armel 1.67.0-13+b1 [229 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67.0 armel 1.67.0-13+b1 [255 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main armel libboost-system1.67-dev armel 1.67.0-13+b1 [232 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem1.67-dev armel 1.67.0-13+b1 [263 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main armel libboost-filesystem-dev armel 1.67.0.2 [4008 B]
Get:94 http://debian.oregonstate.edu/debian unstable/main armel libicu63 armel 63.2-2 [7979 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67.0 armel 1.67.0-13+b1 [454 kB]
Get:96 http://debian.oregonstate.edu/debian unstable/main armel libicu-dev armel 63.2-2 [8922 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main armel libboost-regex1.67-dev armel 1.67.0-13+b1 [556 kB]
Get:98 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-2 [45.3 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-1+b1 [84.7 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67.0 armel 1.67.0-13+b1 [246 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams1.67-dev armel 1.67.0-13+b1 [255 kB]
Get:102 http://debian.oregonstate.edu/debian unstable/main armel libboost-iostreams-dev armel 1.67.0.2 [3956 B]
Get:103 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67.0 armel 1.67.0-13+b1 [332 kB]
Get:104 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options1.67-dev armel 1.67.0-13+b1 [383 kB]
Get:105 http://debian.oregonstate.edu/debian unstable/main armel libboost-program-options-dev armel 1.67.0.2 [3980 B]
Get:106 http://debian.oregonstate.edu/debian unstable/main armel libboost-system-dev armel 1.67.0.2 [4112 B]
Get:107 http://debian.oregonstate.edu/debian unstable/main armel libgenome0 armel 1.3.11+svn20110227.4616-2 [96.5 kB]
Get:108 http://debian.oregonstate.edu/debian unstable/main armel libgenome-dev armel 1.3.11+svn20110227.4616-2 [173 kB]
Get:109 http://debian.oregonstate.edu/debian unstable/main armel libmuscle1 armel 3.7+4565-6 [200 kB]
Get:110 http://debian.oregonstate.edu/debian unstable/main armel libmems1 armel 1.6.0+4725-8+b1 [525 kB]
Get:111 http://debian.oregonstate.edu/debian unstable/main armel libmuscle-dev armel 3.7+4565-6 [256 kB]
Get:112 http://debian.oregonstate.edu/debian unstable/main armel libmems-dev armel 1.6.0+4725-8+b1 [822 kB]
Get:113 http://debian.oregonstate.edu/debian unstable/main amd64 pkgconf amd64 1.6.3-4 [58.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by pkgconf'
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Setting up libxml-sax-base-perl (1.09-1) ...
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Setting up autotools-dev (20180224.1) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
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Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
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Setting up dpkg-cross (2.6.15-3) ...
Setting up crossbuild-essential-armel (12.8) ...
Setting up dh-autoreconf (19) ...
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Setting up libbz2-1.0:armel (1.0.8-2) ...
Setting up libgcc1:armel (1:9.2.1-19) ...
Setting up debhelper (12.7.1) ...
Setting up zlib1g:armel (1:1.2.11.dfsg-1+b1) ...
Setting up libgomp1:armel (9.2.1-19) ...
Setting up libasan5:armel (9.2.1-19) ...
Setting up libatomic1:armel (9.2.1-19) ...
Setting up libstdc++6:armel (9.2.1-19) ...
Setting up libboost-program-options1.67.0:armel (1.67.0-13+b1) ...
Setting up libgenome0:armel (1.3.11+svn20110227.4616-2) ...
Setting up libmuscle1:armel (3.7+4565-6) ...
Setting up libgenome-dev:armel (1.3.11+svn20110227.4616-2) ...
Setting up libicu63:armel (63.2-2) ...
Setting up libmuscle-dev:armel (3.7+4565-6) ...
Setting up libboost-iostreams1.67.0:armel (1.67.0-13+b1) ...
Setting up libubsan1:armel (9.2.1-19) ...
Setting up libboost-system1.67.0:armel (1.67.0-13+b1) ...
Setting up libicu-dev:armel (63.2-2) ...
Setting up libboost-regex1.67.0:armel (1.67.0-13+b1) ...
Setting up libgcc-9-dev:armel (9.2.1-19) ...
Setting up libboost-filesystem1.67.0:armel (1.67.0-13+b1) ...
Setting up libstdc++-9-dev:armel (9.2.1-19) ...
Setting up libmems1:armel (1.6.0+4725-8+b1) ...
Setting up libboost1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-program-options1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-regex1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-program-options-dev:armel (1.67.0.2) ...
Setting up libboost-system1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-dev:armel (1.67.0.2) ...
Setting up libboost-iostreams1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-filesystem1.67-dev:armel (1.67.0-13+b1) ...
Setting up libboost-system-dev:armel (1.67.0.2) ...
Setting up libmems-dev:armel (1.6.0+4725-8+b1) ...
Setting up libboost-iostreams-dev:armel (1.67.0.2) ...
Setting up libboost-filesystem-dev:armel (1.67.0.2) ...
Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3) ...

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

Arch check ok (armel included in any)

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

Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64)
Toolchain package versions: binutils_2.33.1-2 dpkg-dev_1.19.7 g++-8_8.3.0-24 g++-9_9.2.1-19 gcc-8_8.3.0-24 gcc-9_9.2.1-19 libc6-dev_2.29-3 libstdc++-8-dev_8.3.0-24 libstdc++-9-dev_9.2.1-19 libstdc++-9-dev-armel-cross_9.2.1-19cross1 libstdc++6_9.2.1-19 libstdc++6-armel-cross_9.2.1-19cross1 linux-libc-dev_5.3.9-2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2 binutils-arm-linux-gnueabi_2.33.1-2 binutils-common_2.33.1-2 binutils-x86-64-linux-gnu_2.33.1-2 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_8.3.0-24 cpp-9_9.2.1-19 cpp-9-arm-linux-gnueabi_9.2.1-19cross1 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_12.7.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-24 g++-9_9.2.1-19 g++-9-arm-linux-gnueabi_9.2.1-19cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-24 gcc-8-base_8.3.0-24 gcc-9_9.2.1-19 gcc-9-arm-linux-gnueabi_9.2.1-19cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-19cross1 gcc-9-base_9.2.1-19 gcc-9-cross-base_9.2.1-19cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19 libasan5-armel-cross_9.2.1-19cross1 libatomic1_9.2.1-19 libatomic1-armel-cross_9.2.1-19cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-2 libblkid1_2.34-0.1 libboost-dev_1.67.0.2 libboost-filesystem-dev_1.67.0.2 libboost-filesystem1.67-dev_1.67.0-13+b1 libboost-filesystem1.67.0_1.67.0-13+b1 libboost-iostreams-dev_1.67.0.2 libboost-iostreams1.67-dev_1.67.0-13+b1 libboost-iostreams1.67.0_1.67.0-13+b1 libboost-program-options-dev_1.67.0.2 libboost-program-options1.67-dev_1.67.0-13+b1 libboost-program-options1.67.0_1.67.0-13+b1 libboost-regex1.67-dev_1.67.0-13+b1 libboost-regex1.67.0_1.67.0-13+b1 libboost-system-dev_1.67.0.2 libboost-system1.67-dev_1.67.0-13+b1 libboost-system1.67.0_1.67.0-13+b1 libboost1.67-dev_1.67.0-13+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3 libc-dev-bin_2.29-3 libc6_2.29-3 libc6-armel-cross_2.29-1cross7 libc6-dev_2.29-3 libc6-dev-armel-cross_2.29-1cross7 libcap-ng0_0.7.9-2.1+b1 libcc1-0_9.2.1-19 libcom-err2_1.45.4-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-24 libgcc-9-dev_9.2.1-19 libgcc-9-dev-armel-cross_9.2.1-19cross1 libgcc1_1:9.2.1-19 libgcc1-armel-cross_1:9.2.1-19cross1 libgcrypt20_1.8.5-3 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_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19 libgomp1-armel-cross_9.2.1-19cross1 libgpg-error0_1.36-7 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 libisl21_0.21-2 libitm1_9.2.1-19 liblocale-gettext-perl_1.07-4 liblsan0_9.2.1-19 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 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_8.3.0-24 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libquadmath0_9.2.1-19 libseccomp2_2.4.2-2 libselinux1_2.9-3+b1 libsemanage-common_2.9-3 libsemanage1_2.9-3+b1 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.4-1 libstdc++-8-dev_8.3.0-24 libstdc++-9-dev_9.2.1-19 libstdc++-9-dev-armel-cross_9.2.1-19cross1 libstdc++6_9.2.1-19 libstdc++6-armel-cross_9.2.1-19cross1 libsub-override-perl_0.09-2 libsystemd0_243-7 libtasn1-6_4.14-3 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libtsan0_9.2.1-19 libubsan1_9.2.1-19 libubsan1-armel-cross_9.2.1-19cross1 libuchardet0_0.0.6-3 libudev1_243-7 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_2.9.4+dfsg1-7+b4 libyaml-perl_1.29-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.9-2 linux-libc-dev-armel-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.7-2 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_1.6.3-4 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 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-1+b1

+------------------------------------------------------------------------------+
| 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
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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-fcdc2269-e63d-40ba-8546-0f7693651fb9
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_perl: /usr/lib/arm-linux-gnueabi/perl/cross-config-5.30.0/Config.pm does not exist (missing build dependency on perl-xs-dev?)
   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/mfa2xmfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/repeatoire contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/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/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/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/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/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/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/stripSubsetLCBs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/uniquifyTrees 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 2019-11-19T02:15:24Z

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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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Tue, 19 Nov 2019 02:15:23 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.69-11),
 automake (= 1:1.16.1-4),
 autopoint (= 0.19.8.1-9),
 autotools-dev (= 20180224.1),
 base-files (= 11),
 base-passwd (= 3.5.46),
 bash (= 5.0-5),
 binutils (= 2.33.1-2),
 binutils-common (= 2.33.1-2),
 binutils-x86-64-linux-gnu (= 2.33.1-2),
 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 (= 8.3.0-24),
 cpp-9 (= 9.2.1-19),
 dash (= 0.5.10.2-6),
 debconf (= 1.5.73),
 debhelper (= 12.7.1),
 debianutils (= 4.9),
 dh-autoreconf (= 19),
 dh-strip-nondeterminism (= 1.6.2-1),
 diffutils (= 1:3.7-3),
 dpkg (= 1.19.7),
 dpkg-dev (= 1.19.7),
 dwz (= 0.13-2),
 fdisk (= 2.34-0.1),
 file (= 1:5.37-6),
 findutils (= 4.7.0-1),
 g++ (= 4:9.2.1-3.1),
 g++-9 (= 9.2.1-19),
 gcc (= 4:9.2.1-3.1),
 gcc-8 (= 8.3.0-24),
 gcc-8-base (= 8.3.0-24),
 gcc-9 (= 9.2.1-19),
 gcc-9-base (= 9.2.1-19),
 gettext (= 0.19.8.1-9),
 gettext-base (= 0.19.8.1-9),
 grep (= 3.3-1),
 groff-base (= 1.22.4-3),
 gzip (= 1.9-3+b1),
 hostname (= 3.23),
 icu-devtools (= 63.2-2),
 init-system-helpers (= 1.57),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.2.53-5),
 libarchive-zip-perl (= 1.67-1),
 libasan5 (= 9.2.1-19),
 libatomic1 (= 9.2.1-19),
 libattr1 (= 1:2.4.48-5),
 libaudit-common (= 1:2.8.5-2),
 libaudit1 (= 1:2.8.5-2+b1),
 libbinutils (= 2.33.1-2),
 libblkid1 (= 2.34-0.1),
 libboost-dev (= 1.67.0.2),
 libboost-filesystem-dev (= 1.67.0.2),
 libboost-filesystem1.67-dev (= 1.67.0-13+b1),
 libboost-filesystem1.67.0 (= 1.67.0-13+b1),
 libboost-iostreams-dev (= 1.67.0.2),
 libboost-iostreams1.67-dev (= 1.67.0-13+b1),
 libboost-iostreams1.67.0 (= 1.67.0-13+b1),
 libboost-program-options-dev (= 1.67.0.2),
 libboost-program-options1.67-dev (= 1.67.0-13+b1),
 libboost-program-options1.67.0 (= 1.67.0-13+b1),
 libboost-regex1.67-dev (= 1.67.0-13+b1),
 libboost-regex1.67.0 (= 1.67.0-13+b1),
 libboost-system-dev (= 1.67.0.2),
 libboost-system1.67-dev (= 1.67.0-13+b1),
 libboost-system1.67.0 (= 1.67.0-13+b1),
 libboost1.67-dev (= 1.67.0-13+b1),
 libbsd0 (= 0.10.0-1),
 libbz2-1.0 (= 1.0.8-2),
 libc-bin (= 2.29-3),
 libc-dev-bin (= 2.29-3),
 libc6 (= 2.29-3),
 libc6-dev (= 2.29-3),
 libcap-ng0 (= 0.7.9-2.1+b1),
 libcc1-0 (= 9.2.1-19),
 libcroco3 (= 0.6.13-1),
 libdb5.3 (= 5.3.28+dfsg1-0.6),
 libdebconfclient0 (= 0.250),
 libdebhelper-perl (= 12.7.1),
 libdpkg-perl (= 1.19.7),
 libelf1 (= 0.176-1.1),
 libfdisk1 (= 2.34-0.1),
 libffi6 (= 3.2.1-9),
 libfile-stripnondeterminism-perl (= 1.6.2-1),
 libgcc-8-dev (= 8.3.0-24),
 libgcc-9-dev (= 9.2.1-19),
 libgcc1 (= 1:9.2.1-19),
 libgcrypt20 (= 1.8.5-3),
 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 (= 2.62.2-3),
 libgmp10 (= 2:6.1.2+dfsg-4),
 libgomp1 (= 9.2.1-19),
 libgpg-error0 (= 1.36-7),
 libicu-dev (= 63.2-2),
 libicu63 (= 63.2-2),
 libisl21 (= 0.21-2),
 libitm1 (= 9.2.1-19),
 liblsan0 (= 9.2.1-19),
 liblz4-1 (= 1.9.2-2),
 liblzma5 (= 5.2.4-1+b1),
 libmagic-mgc (= 1:5.37-6),
 libmagic1 (= 1:5.37-6),
 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 (= 8.3.0-24),
 libmuscle-dev (= 3.7+4565-6),
 libmuscle1 (= 3.7+4565-6),
 libncurses6 (= 6.1+20191019-1),
 libncursesw6 (= 6.1+20191019-1),
 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 (= 10.32-5+b1),
 libpcre3 (= 2:8.39-12+b1),
 libperl5.30 (= 5.30.0-9),
 libpipeline1 (= 1.5.1-2),
 libquadmath0 (= 9.2.1-19),
 libseccomp2 (= 2.4.2-2),
 libselinux1 (= 2.9-3+b1),
 libsigsegv2 (= 2.12-2),
 libsmartcols1 (= 2.34-0.1),
 libstdc++-8-dev (= 8.3.0-24),
 libstdc++-9-dev (= 9.2.1-19),
 libstdc++6 (= 9.2.1-19),
 libsub-override-perl (= 0.09-2),
 libsystemd0 (= 243-7),
 libtinfo6 (= 6.1+20191019-1),
 libtool (= 2.4.6-11),
 libtsan0 (= 9.2.1-19),
 libubsan1 (= 9.2.1-19),
 libuchardet0 (= 0.0.6-3),
 libudev1 (= 243-7),
 libunistring2 (= 0.9.10-2),
 libuuid1 (= 2.34-0.1),
 libxml2 (= 2.9.4+dfsg1-7+b4),
 linux-libc-dev (= 5.3.9-2),
 login (= 1:4.7-2),
 lsb-base (= 11.1.0),
 m4 (= 1.4.18-4),
 make (= 4.2.1-1.2),
 man-db (= 2.9.0-1),
 mawk (= 1.3.3-17+b3),
 ncurses-base (= 6.1+20191019-1),
 ncurses-bin (= 6.1+20191019-1),
 patch (= 2.7.6-6),
 perl (= 5.30.0-9),
 perl-base (= 5.30.0-9),
 perl-modules-5.30 (= 5.30.0-9),
 pkgconf (= 1.6.3-4),
 po-debconf (= 1.0.21),
 sed (= 4.7-1),
 sensible-utils (= 0.0.12),
 sysvinit-utils (= 2.96-1),
 tar (= 1.30+dfsg-6+b1),
 util-linux (= 2.34-0.1),
 xz-utils (= 5.2.4-1+b1),
 zlib1g (= 1:1.2.11.dfsg-1+b1)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 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 18357372 bytes: control archive=1788 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: 19119
 Depends: progressivemauve (= 1.2.0+4713+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for progressivemauve
 Build-Ids: 013e20dc8cc56c1bbb6650b6926f4a659a606557 02315c5a614e528720ab899c51e45c8ccc1eeaba 271f13713ef23a9cea11e2088346ec1d69ce24cb 31ffa4e2aa405c1bb3d4e79348dd5d4f557ad6f3 350abb7385047165c0961da941583f408d191338 356533f199b7f978afb99a7ed1b9a858848e6a25 3766d4c48ee8d60e213d5b281b98405175c4c6b9 3d8cd96d931fc469a44b591200c17d47202c5910 4c4a14580436233d816e2dd97d7e35c1767bdc42 4e206f8df3e1910be0c99034f957f47c4ca10fee 51682ea732c2cb593670b3104b65339efba53a40 79935bbecb9e15d38ab14c39ed173af85d664274 8b6e5e1c3aee57b11ec13e792260c5969afc9f28 8f12c5e6aeda906b56820f57aed676a39e33339b 9507756478e7f2897a3c9de8eea42cad52df4677 9e1513fa1939347eed7c7c4bba16102f677ee0a9 aa69463ee4faaa177961cf75b8b97d5115af4b2e b361c09c33025e19698f149bf65791c90c20e0df b419b5a5811b1e474f0ea0b80e1f3f8a14ab19fe c77c7caea26b16b1088b81f9164f7992153849d1 d8efa189b3fbc924817e77542ca91fa1defb5b12 e3b16315aa1389c1950f934ce194d0badc2876af e58a63a278d2e09fcf74605052391ea8e2934cb2 e963131ec3d0223c3f2e40d76f6300d3f7c7b41c e9e2ca1df3225ccc898075e380d2d341553ce2d8 ead8a263b1419b5ba7690f693137631629485959 f94b2350fd46aee03f3838dd55218f90b8cac7a3

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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 662408 bytes: control archive=2476 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: 3995
 Depends: libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-program-options1.67.0, libc6 (>= 2.29), libgcc1 (>= 1:3.5), 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.

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drwxr-xr-x root/root         0 2018-12-04 09:03 ./usr/bin/
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-rwxr-xr-x root/root    337428 2018-12-04 09:03 ./usr/bin/bbAnalyze
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-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
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-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
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-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
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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
-------


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

Merged Build-Depends: lintian:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [589 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [672 B]
Fetched 2224 B in 0s (110 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 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
  libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl
  libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-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
  liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl
  libmailtools-perl libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-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:
  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 libfreezethaw-perl
  libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-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
  libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl
  libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-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
  liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl
  libmailtools-perl libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-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, 75 newly installed, 0 to remove and 0 not upgraded.
Need to get 8876 kB of archives.
After this operation, 25.1 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b2 [71.3 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libberkeleydb-perl amd64 0.62-1+b1 [124 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b4 [105 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b3 [38.4 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.43-1 [14.9 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-2 [321 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.42-1 [82.6 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b2 [16.9 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b6 [33.6 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.80+repack-2+b1 [34.8 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.36.0 [1294 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8876 kB in 0s (27.0 MB/s)
Selecting previously unselected package readline-common.
(Reading database ... 35941 files and directories currently installed.)
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Unpacking readline-common (8.0-3) ...
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Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ...
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Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ...
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Setting up libio-async-perl (0.74-1) ...
Setting up patchutils (0.3.4-2+b1) ...
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Setting up libdigest-hmac-perl (1.03+dfsg-2) ...
Setting up libipc-system-simple-perl (1.25-4) ...
Setting up libnet-domain-tld-perl (1.75-1) ...
Setting up t1utils (1.41-3) ...
Setting up liblinux-epoll-perl (0.016-1+b2) ...
Setting up diffstat (1.62-1+b1) ...
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) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsub-name-perl (0.26-1) ...
Setting up libpath-tiny-perl (0.108-1) ...
Setting up librole-tiny-perl (2.001004-1) ...
Setting up netbase (5.6) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006006-1) ...
Setting up libclass-xsaccessor-perl (1.19-3+b3) ...
Setting up libexporter-tiny-perl (1.002001-1) ...
Setting up libclass-accessor-perl (0.51-1) ...
Setting up libnet-ip-perl (1.26-2) ...
Setting up readline-common (8.0-3) ...
Setting up liburi-perl (1.76-1) ...
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Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.36.0) ...
Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ...
Processing triggers for man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.29-3) ...

I: Lintian run was successful.

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| Post Build                                                                   |
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| Summary                                                                      |
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Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 215092
Build-Time: 385
Distribution: unstable
Foreign Architectures: armel
Host Architecture: armel
Install-Time: 22
Job: progressivemauve_1.2.0+4713+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: progressivemauve
Package-Time: 420
Source-Version: 1.2.0+4713+dfsg-4
Space: 215092
Status: successful
Version: 1.2.0+4713+dfsg-4
--------------------------------------------------------------------------------
Finished at 2019-11-19T02:15:24Z
Build needed 00:07:00, 215092k disk space