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

+==============================================================================+
| sga 0.10.15-7 (armel)                        Sun, 03 Oct 2021 10:30:47 +0000 |
+==============================================================================+

Package: sga
Version: 0.10.15-7
Source Version: 0.10.15-7
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-ff5d8562-aeda-4231-b344-e44776b1cac5' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/sga-sOU40R/resolver-VBA2hW' with '<<RESOLVERDIR>>'

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

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-10-03-0801.08-F-2021-10-03-0801.08.pdiff [4223 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-10-03-0801.08-F-2021-10-03-0801.08.pdiff [2723 B]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-10-03-0801.08-F-2021-10-03-0801.08.pdiff [4223 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-10-03-0801.08-F-2021-10-03-0801.08.pdiff [2723 B]
Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [8405 kB]
Fetched 8705 kB in 3s (3261 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: 'sga' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/sga.git
Please use:
git clone https://salsa.debian.org/med-team/sga.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 6786 kB of source archives.
Get:1 http://debian.oregonstate.edu/debian unstable/main sga 0.10.15-7 (dsc) [2084 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main sga 0.10.15-7 (tar) [6570 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main sga 0.10.15-7 (diff) [214 kB]
Fetched 6786 kB in 0s (108 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/sga-sOU40R/sga-0.10.15' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/sga-sOU40R' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel
Filtered Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev, libbamtools-dev, help2man, 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 [476 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [528 B]
Fetched 1961 B in 0s (85.6 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
  bsdextrautils build-essential cpp-10-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10
  g++-10-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-arm-linux-gnueabi
  gcc-10-arm-linux-gnueabi-base gcc-10-cross-base gcc-11-base:armel
  gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext
  gettext-base groff-base help2man intltool-debian libarchive-zip-perl
  libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross
  libbamtools-dev:armel libbamtools2.5.1:armel libc6:armel libc6-armel-cross
  libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel
  libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel
  libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl
  libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl
  libfile-which-perl libgcc-10-dev-armel-cross libgcc-9-dev:armel
  libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross
  libgssapi-krb5-2:armel libicu67 libio-string-perl libk5crypto3:armel
  libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel
  liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnsl-dev
  libnsl-dev:armel libnsl2:armel libperl5.32 libpipeline1 libpython3-stdlib
  libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsparsehash-dev
  libsqlite3-0 libssl1.1:armel libstdc++-10-dev libstdc++-10-dev-armel-cross
  libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtirpc-dev libtirpc-dev:armel libtirpc3:armel 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 media-types perl perl-modules-5.32
  po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
  python3.9 python3.9-minimal rpcsvc-proto sensible-utils ucf zlib1g:armel
  zlib1g-dev:armel
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib
  g++-10-multilib gcc-10-doc manpages-dev flex bison gdb-arm-linux-gnueabi
  gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff
  libbamtools-doc:armel glibc-doc:armel libc-l10n:armel locales:armel
  libnss-nis:armel libnss-nisplus:armel glibc-doc manpages-dev:armel gnupg git
  bzr krb5-doc:armel krb5-user:armel libstdc++-10-doc libstdc++-9-doc:armel
  libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc
  apparmor less www-browser perl-doc libterm-readline-gnu-perl
  | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl
  python3-doc python3-tk python3-venv python3.9-venv python3.9-doc
  binfmt-support
Recommended packages:
  gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:armel
  libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:armel
  ca-certificates libltdl-dev libwww-perl libxml-sax-expat-perl
  libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi
  bsdextrautils build-essential cpp-10-arm-linux-gnueabi cpp-arm-linux-gnueabi
  cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10
  g++-10-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-arm-linux-gnueabi
  gcc-10-arm-linux-gnueabi-base gcc-10-cross-base gcc-11-base:armel
  gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext
  gettext-base groff-base help2man intltool-debian libarchive-zip-perl
  libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross
  libbamtools-dev:armel libbamtools2.5.1:armel libc6:armel libc6-armel-cross
  libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel
  libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel
  libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl
  libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl
  libfile-which-perl libgcc-10-dev-armel-cross libgcc-9-dev:armel
  libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross
  libgssapi-krb5-2:armel libicu67 libio-string-perl libk5crypto3:armel
  libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel
  liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnsl-dev
  libnsl-dev:armel libnsl2:armel libperl5.32 libpipeline1 libpython3-stdlib
  libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsparsehash-dev
  libsqlite3-0 libssl1.1:armel libstdc++-10-dev libstdc++-10-dev-armel-cross
  libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtirpc-dev libtirpc-dev:armel libtirpc3:armel 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 media-types perl perl-modules-5.32
  po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
  python3.9 python3.9-minimal rpcsvc-proto
  sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel
  zlib1g-dev:armel
0 upgraded, 130 newly installed, 0 to remove and 0 not upgraded.
Need to get 222 MB of archives.
After this operation, 949 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.2-3 [143 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-7 [935 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-2 [1354 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-6 [2824 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-6 [4106 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-6 [293 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-minimal amd64 3.9.7-4 [804 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.4.1-2+b1 [104 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9-minimal amd64 3.9.7-4 [1963 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 media-types all 4.0.0 [30.3 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-stdlib amd64 3.9.7-4 [1688 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9 amd64 3.9.7-4 [480 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.9.2-3 [37.9 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main armel gcc-11-base armel 11.2.0-8 [205 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.4.0-3 [200 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.39-3 [126 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.39-3 [69.1 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.4-2 [819 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.37-7 [2865 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.25-2 [104 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.32-4 [2251 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev amd64 10.3.0-11 [1750 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10 amd64 10.3.0-11 [9434 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:10.2.1-1 [1644 B]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.9 [1537 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.9 [2153 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-arm-linux-gnueabi-base amd64 10.3.0-8cross1 [205 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-10-arm-linux-gnueabi amd64 10.3.0-8cross1 [44.1 MB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:10.2.1-1 [16.8 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.3.0-8cross1 [200 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base all 11.2.0-5cross1 [201 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.32-1cross4 [1121 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 11.2.0-5cross1 [38.5 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 11.2.0-5cross1 [88.9 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 11.2.0-5cross1 [8804 B]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-armel-cross all 11.2.0-5cross1 [1935 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 11.2.0-5cross1 [426 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 11.2.0-5cross1 [796 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-10-dev-armel-cross all 10.3.0-8cross1 [687 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-arm-linux-gnueabi amd64 10.3.0-8cross1 [50.4 MB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:10.2.1-1 [1460 B]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.10.46-4cross4 [1436 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.32-1cross4 [1801 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev-armel-cross all 10.3.0-8cross1 [1758 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10-arm-linux-gnueabi amd64 10.3.0-8cross1 [47.2 MB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:10.2.1-1 [1176 B]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.9 [6704 B]
Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.5.2 [192 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.185-2 [172 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB]
Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.5.2 [1056 kB]
Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 python3-distutils all 3.9.7-1 [146 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.48.5 [143 kB]
Get:102 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 11.2.0-8 [38.4 kB]
Get:103 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.32-4 [2349 kB]
Get:104 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.4.0-3 [2703 kB]
Get:105 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 11.2.0-8 [9012 B]
Get:106 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 11.2.0-8 [466 kB]
Get:107 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB]
Get:108 http://debian.oregonstate.edu/debian unstable/main armel libbamtools2.5.1 armel 2.5.1+dfsg-9 [134 kB]
Get:109 http://debian.oregonstate.edu/debian unstable/main armel libbamtools-dev armel 2.5.1+dfsg-9 [190 kB]
Get:110 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.14.6-3 [1385 kB]
Get:111 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.25-2 [98.8 kB]
Get:112 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.25-2 [115 kB]
Get:113 http://debian.oregonstate.edu/debian unstable/main armel libcom-err2 armel 1.46.4-1 [74.5 kB]
Get:114 http://debian.oregonstate.edu/debian unstable/main armel libkrb5support0 armel 1.18.3-7 [62.4 kB]
Get:115 http://debian.oregonstate.edu/debian unstable/main armel libk5crypto3 armel 1.18.3-7 [108 kB]
Get:116 http://debian.oregonstate.edu/debian unstable/main armel libkeyutils1 armel 1.6.1-2 [14.5 kB]
Get:117 http://debian.oregonstate.edu/debian unstable/main armel libssl1.1 armel 1.1.1l-1 [1279 kB]
Get:118 http://debian.oregonstate.edu/debian unstable/main armel libkrb5-3 armel 1.18.3-7 [315 kB]
Get:119 http://debian.oregonstate.edu/debian unstable/main armel libgssapi-krb5-2 armel 1.18.3-7 [142 kB]
Get:120 http://debian.oregonstate.edu/debian unstable/main armel libtirpc3 armel 1.3.2-2 [71.6 kB]
Get:121 http://debian.oregonstate.edu/debian unstable/main armel libnsl2 armel 1.3.0-2 [33.0 kB]
Get:122 http://debian.oregonstate.edu/debian unstable/main armel libtirpc-dev armel 1.3.2-2 [182 kB]
Get:123 http://debian.oregonstate.edu/debian unstable/main armel libnsl-dev armel 1.3.0-2 [61.7 kB]
Get:124 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.32-4 [1849 kB]
Get:125 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 11.2.0-8 [90.7 kB]
Get:126 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 11.2.0-8 [797 kB]
Get:127 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.4.0-3 [641 kB]
Get:128 http://debian.oregonstate.edu/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:129 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.4.0-3 [1761 kB]
Get:130 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libconfig-inifiles-perl (3.000003-1) ...
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Setting up bsdextrautils (2.37.2-3) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:amd64 (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up perl-modules-5.32 (5.32.1-6) ...
Setting up libsqlite3-0:amd64 (3.36.0-2) ...
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Setting up linux-libc-dev:armel (5.14.6-3) ...
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Setting up linux-libc-dev-armel-cross (5.10.46-4cross4) ...
Setting up autotools-dev (20180224.1+nmu1) ...
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Setting up rpcsvc-proto (1.4.2-4) ...
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Setting up libperl5.32:amd64 (5.32.1-6) ...
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Setting up libc6-armel-cross (2.32-1cross4) ...
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Setting up libnsl-dev:amd64 (1.3.0-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libcrypt-dev:amd64 (1:4.4.25-2) ...
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Setting up libmpdec3:amd64 (2.5.1-2) ...
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Setting up perl (5.32.1-6) ...
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update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) 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
Setting up libxml-libxml-perl (2.0134+dfsg-2+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 crossbuild-essential-armel (12.9) ...
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Setting up libkeyutils1:armel (1.6.1-2) ...
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Setting up zlib1g:armel (1:1.2.11.dfsg-2) ...
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Setting up libcom-err2:armel (1.46.4-1) ...
Setting up libgomp1:armel (11.2.0-8) ...
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Setting up libasan5:armel (9.4.0-3) ...
Setting up libbamtools2.5.1:armel (2.5.1+dfsg-9) ...
Setting up libatomic1:armel (11.2.0-8) ...
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Setting up libcrypt-dev:armel (1:4.4.25-2) ...
Setting up libkrb5-3:armel (1.18.3-7) ...
Setting up libgcc-9-dev:armel (9.4.0-3) ...
Setting up libbamtools-dev:armel (2.5.1+dfsg-9) ...
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Setting up libnsl2:armel (1.3.0-2) ...
Setting up libnsl-dev:armel (1.3.0-2) ...
Setting up libc6-dev:armel (2.32-4) ...
Setting up libstdc++-9-dev:armel (9.4.0-3) ...
Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ...
Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4) ...

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

Arch check ok (armel included in any)

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

Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64)
Toolchain package versions: binutils_2.37-7 dpkg-dev_1.20.9 g++-10_10.3.0-11 gcc-10_10.3.0-11 libc6-dev_2.32-4 libstdc++-10-dev_10.3.0-11 libstdc++-10-dev-armel-cross_10.3.0-8cross1 libstdc++-9-dev_9.4.0-3 libstdc++6_11.2.0-8 libstdc++6-armel-cross_11.2.0-5cross1 linux-libc-dev_5.14.6-3
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b1 binutils_2.37-7 binutils-arm-linux-gnueabi_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-3 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4+b1 cpp_4:10.2.1-1 cpp-10_10.3.0-11 cpp-10-arm-linux-gnueabi_10.3.0-8cross1 cpp-8_8.4.0-7 cpp-arm-linux-gnueabi_4:10.2.1-1 cross-config_2.6.18+nmu2 crossbuild-essential-armel_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-python_4.20201102+nmu1 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.20.9 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.26-1 fdisk_2.37.2-3 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.3.0-11 g++-10-arm-linux-gnueabi_10.3.0-8cross1 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libc6-dev-armel-cross_2.32-1cross4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-8 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.20.9 libelf1_0.185-2 libexpat1_2.4.1-2+b1 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libfdisk1_2.37.2-3 libffi6_3.2.1-9 libffi8_3.4.2-2 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libgcc-10-dev_10.3.0-11 libgcc-10-dev-armel-cross_10.3.0-8cross1 libgcc-9-dev_9.4.0-3 libgcc-s1_11.2.0-8 libgcc-s1-armel-cross_11.2.0-5cross1 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-8 libgomp1-armel-cross_11.2.0-5cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl19_0.20-2 libisl23_0.23-1 libitm1_11.2.0-8 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-8 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-3 libmpc3_1.2.0-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libmpx2_8.4.0-7 libncursesw6_6.2+20210905-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-3 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.28_5.28.1-6 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libquadmath0_11.2.0-8 libreadline8_8.1-2 libseccomp2_2.5.2-1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-3 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11 libstdc++-10-dev-armel-cross_10.3.0-8cross1 libstdc++-9-dev_9.4.0-3 libstdc++6_11.2.0-8 libstdc++6-armel-cross_11.2.0-5cross1 libsub-override-perl_0.09-2 libsystemd0_247.9-4 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-8 libubsan1_11.2.0-8 libubsan1-armel-cross_11.2.0-5cross1 libuchardet0_0.0.7-1 libudev1_247.9-4 libunistring2_0.9.10-6 libuuid1_2.37.2-3 libxml-libxml-perl_2.0134+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libyaml-perl_1.30-1 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.14.6-3 linux-libc-dev-armel-cross_5.10.46-4cross4 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-3 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.28_5.28.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3.9_3.9.7-4 python3.9-minimal_3.9.7-4 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021c-1 ucf_3.0043 util-linux_2.37.2-3 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

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


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

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: sga
Binary: sga
Architecture: any
Version: 0.10.15-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/jts/sga
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/sga
Vcs-Git: https://salsa.debian.org/med-team/sga.git
Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools <!nocheck>, python3 <!nocheck>, python3-ruffus <!nocheck>, python3-pysam <!nocheck>
Package-List:
 sga deb science optional arch=any
Checksums-Sha1:
 55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz
 4598b0bf58446b932f202a8bfa7e9d9d3bc018de 214356 sga_0.10.15-7.debian.tar.xz
Checksums-Sha256:
 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 6569986 sga_0.10.15.orig.tar.gz
 708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 214356 sga_0.10.15-7.debian.tar.xz
Files:
 990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz
 420c1f46b48f89950ac7e500402215e8 214356 sga_0.10.15-7.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.jeR6Ze68/trustedkeys.kbx': General error
gpgv: Signature made Fri Sep 17 14:05:16 2021 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./sga_0.10.15-7.dsc
dpkg-source: info: extracting sga in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz
dpkg-source: info: unpacking sga_0.10.15-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0002-no-rpath.patch
dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch
dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch
dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch
dpkg-source: info: applying 0006-remove-google-addsense.patch
dpkg-source: info: applying gcc-7.patch
dpkg-source: info: applying no_privacy_breach_url.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying no_enforcing_c++98.patch
dpkg-source: info: applying gcc9.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-ff5d8562-aeda-4231-b344-e44776b1cac5
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 sga
dpkg-buildpackage: info: source version 0.10.15-7
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@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
 debian/rules clean
dh clean --with python3 --sourcedirectory=src
   dh_auto_clean -O--sourcedirectory=src
   dh_autoreconf_clean -O--sourcedirectory=src
   dh_clean -O--sourcedirectory=src
 debian/rules binary-arch
dh binary-arch --with python3 --sourcedirectory=src
   dh_update_autotools_config -a -O--sourcedirectory=src
   dh_autoreconf -a -O--sourcedirectory=src
configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:7: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:7: the top level
configure.ac:24: warning: The macro `AC_TRY_LINK' is obsolete.
configure.ac:24: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/m4_ax_openmp.m4:70: AX_OPENMP is expanded from...
configure.ac:24: the top level
configure.ac:12: installing './compile'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
Algorithm/Makefile.am: installing './depcomp'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --with-bamtools=/usr/
	cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi --with-bamtools=/usr/
configure: loading site script /etc/dpkg-cross/cross-config.armel
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 race-free 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-g++... arm-linux-gnueabi-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... yes
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether arm-linux-gnueabi-g++ accepts -g... yes
checking for arm-linux-gnueabi-g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of arm-linux-gnueabi-g++... none
checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc
checking whether the compiler supports GNU C... yes
checking whether arm-linux-gnueabi-gcc accepts -g... yes
checking for arm-linux-gnueabi-gcc option to enable C11 features... none needed
checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes
checking dependency style of arm-linux-gnueabi-gcc... none
checking for arm-linux-gnueabi-ranlib... arm-linux-gnueabi-ranlib
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing clock_gettime... none required
checking for OpenMP flag of C++ compiler... -fopenmp
checking for host type... you are not using osx so multi-threading should work.
checking for google/sparse_hash_set... yes
checking for google/sparse_hash_set... (cached) yes
checking for google/sparse_hash_map... yes
checking for unordered_map... yes
checking for tr1/unordered_map... yes
checking for ext/hash_map... yes
checking for unordered_set... yes
checking for tr1/unordered_set... yes
checking for ext/hash_set... yes
checking for api/BamReader.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating Thirdparty/Makefile
config.status: creating Util/Makefile
config.status: creating SQG/Makefile
config.status: creating Bigraph/Makefile
config.status: creating Algorithm/Makefile
config.status: creating StringGraph/Makefile
config.status: creating Concurrency/Makefile
config.status: creating SuffixTools/Makefile
config.status: creating GraphDiff/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SGA/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_build -a -O--sourcedirectory=src
	cd src && make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make  all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Making all in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/bin'
cp -n sga-bam2de.pl sga-bam2de
cp -n sga-mergeDriver.pl sga-mergeDriver
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/bin'
Making all in Thirdparty
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Thirdparty'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gzstream.o gzstream.C
arm-linux-gnueabi-gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools  -std=gnu99 -O3 -c -o stdaln.o stdaln.c
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o overlapper.o overlapper.cpp
overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers]
   37 | OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP };
      |                                                                ^
overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers]
   38 | OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP };
      |                                                                     ^
overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers]
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o multiple_alignment.o multiple_alignment.cpp
arm-linux-gnueabi-gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools  -std=gnu99 -O3 -c -o bcr.o bcr.c
bcr.c: In function ‘ld_restore’:
bcr.c:183:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  183 |  fread(&ld->max, sizeof(int), 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bcr.c:186:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  186 |   fread(&x, sizeof(int), 1, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bcr.c:189:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  189 |    fread(ld->a[i], 8, x, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MurmurHash3.o MurmurHash3.cpp
MurmurHash3.cpp: In function ‘void MurmurHash3_x86_32(const void*, int, uint32_t, void*)’:
MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
  132 |   case 3: k1 ^= tail[2] << 16;
      |           ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:133:3: note: here
  133 |   case 2: k1 ^= tail[1] << 8;
      |   ^~~~
MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
  133 |   case 2: k1 ^= tail[1] << 8;
      |           ~~~^~~~~~~~~~~~~~~
MurmurHash3.cpp:134:3: note: here
  134 |   case 1: k1 ^= tail[0];
      |   ^~~~
MurmurHash3.cpp: In function ‘void MurmurHash3_x86_128(const void*, int, uint32_t, void*)’:
MurmurHash3.cpp:207:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  207 |   case 15: k4 ^= tail[14] << 16;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:208:3: note: here
  208 |   case 14: k4 ^= tail[13] << 8;
      |   ^~~~
MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  208 |   case 14: k4 ^= tail[13] << 8;
      |            ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:209:3: note: here
  209 |   case 13: k4 ^= tail[12] << 0;
      |   ^~~~
MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
  210 |            k4 *= c4; k4  = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
      |                                                     ~~~^~~~~
MurmurHash3.cpp:212:3: note: here
  212 |   case 12: k3 ^= tail[11] << 24;
      |   ^~~~
MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  212 |   case 12: k3 ^= tail[11] << 24;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:213:3: note: here
  213 |   case 11: k3 ^= tail[10] << 16;
      |   ^~~~
MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  213 |   case 11: k3 ^= tail[10] << 16;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:214:3: note: here
  214 |   case 10: k3 ^= tail[ 9] << 8;
      |   ^~~~
MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  214 |   case 10: k3 ^= tail[ 9] << 8;
      |            ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:215:3: note: here
  215 |   case  9: k3 ^= tail[ 8] << 0;
      |   ^~~~
MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
  216 |            k3 *= c3; k3  = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
      |                                                     ~~~^~~~~
MurmurHash3.cpp:218:3: note: here
  218 |   case  8: k2 ^= tail[ 7] << 24;
      |   ^~~~
MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  218 |   case  8: k2 ^= tail[ 7] << 24;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:219:3: note: here
  219 |   case  7: k2 ^= tail[ 6] << 16;
      |   ^~~~
MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  219 |   case  7: k2 ^= tail[ 6] << 16;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:220:3: note: here
  220 |   case  6: k2 ^= tail[ 5] << 8;
      |   ^~~~
MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  220 |   case  6: k2 ^= tail[ 5] << 8;
      |            ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:221:3: note: here
  221 |   case  5: k2 ^= tail[ 4] << 0;
      |   ^~~~
MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
  222 |            k2 *= c2; k2  = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
      |                                                     ~~~^~~~~
MurmurHash3.cpp:224:3: note: here
  224 |   case  4: k1 ^= tail[ 3] << 24;
      |   ^~~~
MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  224 |   case  4: k1 ^= tail[ 3] << 24;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:225:3: note: here
  225 |   case  3: k1 ^= tail[ 2] << 16;
      |   ^~~~
MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  225 |   case  3: k1 ^= tail[ 2] << 16;
      |            ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:226:3: note: here
  226 |   case  2: k1 ^= tail[ 1] << 8;
      |   ^~~~
MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  226 |   case  2: k1 ^= tail[ 1] << 8;
      |            ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:227:3: note: here
  227 |   case  1: k1 ^= tail[ 0] << 0;
      |   ^~~~
MurmurHash3.cpp: In function ‘void MurmurHash3_x64_128(const void*, int, uint32_t, void*)’:
MurmurHash3.cpp:296:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  296 |   case 15: k2 ^= uint64_t(tail[14]) << 48;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:297:3: note: here
  297 |   case 14: k2 ^= uint64_t(tail[13]) << 40;
      |   ^~~~
MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  297 |   case 14: k2 ^= uint64_t(tail[13]) << 40;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:298:3: note: here
  298 |   case 13: k2 ^= uint64_t(tail[12]) << 32;
      |   ^~~~
MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  298 |   case 13: k2 ^= uint64_t(tail[12]) << 32;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:299:3: note: here
  299 |   case 12: k2 ^= uint64_t(tail[11]) << 24;
      |   ^~~~
MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  299 |   case 12: k2 ^= uint64_t(tail[11]) << 24;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:300:3: note: here
  300 |   case 11: k2 ^= uint64_t(tail[10]) << 16;
      |   ^~~~
MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  300 |   case 11: k2 ^= uint64_t(tail[10]) << 16;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:301:3: note: here
  301 |   case 10: k2 ^= uint64_t(tail[ 9]) << 8;
      |   ^~~~
MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  301 |   case 10: k2 ^= uint64_t(tail[ 9]) << 8;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:302:3: note: here
  302 |   case  9: k2 ^= uint64_t(tail[ 8]) << 0;
      |   ^~~~
MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
  303 |            k2 *= c2; k2  = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
      |                                                     ~~~^~~~~
MurmurHash3.cpp:305:3: note: here
  305 |   case  8: k1 ^= uint64_t(tail[ 7]) << 56;
      |   ^~~~
MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  305 |   case  8: k1 ^= uint64_t(tail[ 7]) << 56;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:306:3: note: here
  306 |   case  7: k1 ^= uint64_t(tail[ 6]) << 48;
      |   ^~~~
MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  306 |   case  7: k1 ^= uint64_t(tail[ 6]) << 48;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:307:3: note: here
  307 |   case  6: k1 ^= uint64_t(tail[ 5]) << 40;
      |   ^~~~
MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  307 |   case  6: k1 ^= uint64_t(tail[ 5]) << 40;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:308:3: note: here
  308 |   case  5: k1 ^= uint64_t(tail[ 4]) << 32;
      |   ^~~~
MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  308 |   case  5: k1 ^= uint64_t(tail[ 4]) << 32;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:309:3: note: here
  309 |   case  4: k1 ^= uint64_t(tail[ 3]) << 24;
      |   ^~~~
MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  309 |   case  4: k1 ^= uint64_t(tail[ 3]) << 24;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:310:3: note: here
  310 |   case  3: k1 ^= uint64_t(tail[ 2]) << 16;
      |   ^~~~
MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  310 |   case  3: k1 ^= uint64_t(tail[ 2]) << 16;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:311:3: note: here
  311 |   case  2: k1 ^= uint64_t(tail[ 1]) << 8;
      |   ^~~~
MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
  311 |   case  2: k1 ^= uint64_t(tail[ 1]) << 8;
      |            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:312:3: note: here
  312 |   case  1: k1 ^= uint64_t(tail[ 0]) << 0;
      |   ^~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o count_min_sketch.o count_min_sketch.cpp
rm -f libthirdparty.a
ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libthirdparty.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Thirdparty'
Making all in Util
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Util'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp
Alphabet.cpp:101:84: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  101 | template<> const size_t AlphaCount64::maxValue = std::numeric_limits<uint64_t>::max();
      |                                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from Util.h:12,
                 from Match.h:13,
                 from MultiOverlap.h:13,
                 from MultiOverlap.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MultiOverlap::MOData&}; _Tp = MultiOverlap::MOData; _Alloc = std::allocator<MultiOverlap::MOData>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MultiOverlap::MOData>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from Util.h:12,
                 from Match.h:13,
                 from MultiOverlap.h:13,
                 from MultiOverlap.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void MultiOverlap::add(const string&, const Overlap&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void MultiOverlap::add(const MultiOverlap::MOData&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from Util.h:12,
                 from Match.h:13,
                 from MultiOverlap.h:13,
                 from MultiOverlap.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AlphaCount<long long unsigned int>&}; _Tp = AlphaCount<long long unsigned int>; _Alloc = std::allocator<AlphaCount<long long unsigned int> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<AlphaCount<long long unsigned int> >::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator<PUElem>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PUElem>::iterator’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator<PUElem>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PUElem*, std::vector<PUElem> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from MultiOverlap.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from MultiOverlap.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >; _Distance = int; _Tp = MultiOverlap::MOData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from MultiOverlap.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In member function ‘void MultiOverlap::print(int, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MultiOverlap::MOData*, std::vector<MultiOverlap::MOData> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from Util.h:12,
                 from Match.h:13,
                 from MultiOverlap.h:13,
                 from MultiOverlap.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘std::string MultiOverlap::consensusConflict(double, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AlphaCount<long long unsigned int>*, std::vector<AlphaCount<long long unsigned int> > >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from QualityVector.h:13,
                 from QualityVector.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DNADouble&}; _Tp = DNADouble; _Alloc = std::allocator<DNADouble>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DNADouble>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from QualityVector.h:13,
                 from QualityVector.cpp:13:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void QualityVector::add(DNADouble)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DNADouble*, std::vector<DNADouble> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from Quality.h:13,
                 from Quality.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from Quality.h:13,
                 from Quality.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘DoubleVector Quality::uniformLogProbVector(double, size_t)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from VCFUtil.h:14,
                 from VCFUtil.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator<VCFRecord>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<VCFRecord>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from VCFUtil.h:14,
                 from VCFUtil.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const string&, const string&, const string&, const string&, size_t, const string&, int, double, int, VCFVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<VCFRecord*, std::vector<VCFRecord> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp
rm -f libutil.a
ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libutil.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Util'
Making all in SQG
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SQG'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp
rm -f libsqg.a
ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libsqg.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/SQG'
Making all in Bigraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Bigraph'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp
In file included from ../Util/EncodedString.h:22,
                 from Vertex.h:23,
                 from Vertex.cpp:9:
../Util/EncodedString.h: In instantiation of ‘void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]’:
../Util/EncodedString.h:43:18:   required from ‘EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]’
Vertex.cpp:34:46:   required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  236 |             assert(m_capacity = other.m_capacity);
      |                    ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp
rm -f libbigraph.a
ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libbigraph.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Bigraph'
Making all in Algorithm
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Algorithm'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:944:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
  944 |     __unique(_ForwardIterator __first, _ForwardIterator __last,
      |     ^~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:944:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SearchSeed&}; _Tp = SearchSeed; _Alloc = std::allocator<SearchSeed>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SearchSeed>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/list:64,
                 from ../Util/Util.h:13,
                 from ../Util/Alphabet.h:29,
                 from ../SuffixTools/STGlobals.h:19,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/list.tcc: In member function ‘std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(std::__cxx11::list<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator<OverlapBlock>; <template-parameter-2-2> = void; _Tp = OverlapBlock; _Alloc = std::allocator<OverlapBlock>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::const_iterator’ changed in GCC 7.1
  133 |       list<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
OverlapAlgorithm.cpp: In member function ‘OverlapResult OverlapAlgorithm::overlapReadExact(const SeqRecord&, int, OverlapBlockList*) const’:
OverlapAlgorithm.cpp:150:87: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::const_iterator’ changed in GCC 7.1
  150 |     oblSuffixFwd.insert(oblSuffixFwd.end(), oblFwdContain.begin(), oblFwdContain.end());
      |                                                                                       ^
OverlapAlgorithm.cpp:150:87: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
OverlapAlgorithm.cpp:151:87: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::const_iterator’ changed in GCC 7.1
  151 |     oblPrefixFwd.insert(oblPrefixFwd.end(), oblFwdContain.begin(), oblFwdContain.end());
      |                                                                                       ^
OverlapAlgorithm.cpp:151:87: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
OverlapAlgorithm.cpp:152:87: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::const_iterator’ changed in GCC 7.1
  152 |     oblSuffixRev.insert(oblSuffixRev.end(), oblRevContain.begin(), oblRevContain.end());
      |                                                                                       ^
OverlapAlgorithm.cpp:152:87: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
OverlapAlgorithm.cpp:153:87: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::const_iterator’ changed in GCC 7.1
  153 |     oblPrefixRev.insert(oblPrefixRev.end(), oblRevContain.begin(), oblRevContain.end());
      |                                                                                       ^
OverlapAlgorithm.cpp:153:87: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
   79 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _Distance = int; _Tp = SearchSeed; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const SearchSeed&, const SearchSeed&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1929 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1930 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from OverlapAlgorithm.cpp:6:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1020:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SearchSeed*, std::vector<SearchSeed> >’ changed in GCC 7.1
 1020 |       return std::__unique(__first, __last,
      |              ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1021 |       __gnu_cxx::__ops::__iter_comp_iter(__binary_pred));
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/list:63,
                 from ../SuffixTools/BWTInterval.h:13,
                 from OverlapBlock.h:14,
                 from OverlapBlock.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const OverlapBlock&}; _Tp = OverlapBlock; _Alloc = std::allocator<OverlapBlock>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list<OverlapBlock>::iterator’ changed in GCC 7.1
 1909 |        _M_insert(iterator __position, _Args&&... __args)
      |        ^~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:60,
                 from ../SuffixTools/STGlobals.h:15,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapBlock.h:17,
                 from OverlapBlock.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In 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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator’ changed in GCC 7.1
 2460 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/list:63,
                 from ../SuffixTools/BWTInterval.h:13,
                 from OverlapBlock.h:14,
                 from OverlapBlock.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_list.h: In function ‘OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator<OverlapBlock>’ changed in GCC 7.1
 1212 |       { this->_M_insert(end(), __x); }
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:61,
                 from ../SuffixTools/STGlobals.h:15,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapBlock.h:17,
                 from OverlapBlock.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:60,
                 from ../SuffixTools/STGlobals.h:15,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ErrorCorrectProcess.h:14,
                 from ErrorCorrectProcess.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In 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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, ErrorCount>; _KeyOfValue = std::_Select1st<std::pair<const long long int, ErrorCount> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, ErrorCount> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, ErrorCount>, std::_Select1st<std::pair<const long long int, ErrorCount> >, std::less<long long int>, std::allocator<std::pair<const long long int, ErrorCount> > >::const_iterator’ changed in GCC 7.1
 2460 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In 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 char&>, std::tuple<>}; _Key = char; _Val = std::pair<const char, ErrorCount>; _KeyOfValue = std::_Select1st<std::pair<const char, ErrorCount> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, ErrorCount> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<char, std::pair<const char, ErrorCount>, std::_Select1st<std::pair<const char, ErrorCount> >, std::less<char>, std::allocator<std::pair<const char, ErrorCount> > >::const_iterator’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, ErrorCount>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2195:5: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ErrorCount>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> > >::const_iterator’ changed in GCC 7.1
 2195 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In 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>, ErrorCount>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ErrorCount>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> > >::const_iterator’ changed in GCC 7.1
 2460 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ErrorCount>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> > >::const_iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:61,
                 from ../SuffixTools/STGlobals.h:15,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ErrorCorrectProcess.h:14,
                 from ErrorCorrectProcess.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h: In member function ‘void ErrorCorrectPostProcess::collectMetrics(const string&, const string&, const string&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, ErrorCount>, std::_Select1st<std::pair<const long long int, ErrorCount> >, std::less<long long int>, std::allocator<std::pair<const long long int, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<char, std::pair<const char, ErrorCount>, std::_Select1st<std::pair<const char, ErrorCount> >, std::less<char>, std::allocator<std::pair<const char, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<char, std::pair<const char, ErrorCount>, std::_Select1st<std::pair<const char, ErrorCount> >, std::less<char>, std::allocator<std::pair<const char, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ErrorCount>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, ErrorCount>, std::_Select1st<std::pair<const long long int, ErrorCount> >, std::less<long long int>, std::allocator<std::pair<const long long int, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<char, std::pair<const char, ErrorCount>, std::_Select1st<std::pair<const char, ErrorCount> >, std::less<char>, std::allocator<std::pair<const char, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<char, std::pair<const char, ErrorCount>, std::_Select1st<std::pair<const char, ErrorCount> >, std::less<char>, std::allocator<std::pair<const char, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ErrorCount>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ErrorCount> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from FMMergeProcess.h:12,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator<BWTInterval>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BWTInterval>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from FMMergeProcess.h:13,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
   79 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from FMMergeProcess.h:13,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Distance = int; _Tp = BWTInterval; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from FMMergeProcess.h:13,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1667 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BWTInterval&, const BWTInterval&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1929 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1930 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1942 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/Util.h:12,
                 from FMMergeProcess.h:12,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from FMMergeProcess.h:13,
                 from FMMergeProcess.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from ReadCluster.h:13,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ClusterNode&}; _Tp = ClusterNode; _Alloc = std::allocator<ClusterNode>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ClusterNode>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ReadCluster.h:14,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:944:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
  944 |     __unique(_ForwardIterator __first, _ForwardIterator __last,
      |     ^~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:944:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
In file included from ReadCluster.cpp:10:
ReadCluster.h: In member function ‘ClusterNode ReadCluster::addSeed(const string&, bool)’:
ReadCluster.h:17:8: warning: ‘emptyNode.ClusterNode::fwdCanonicalID’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   17 | struct ClusterNode
      |        ^~~~~~~~~~~
ReadCluster.h:17:8: warning: ‘emptyNode.ClusterNode::isReverseInterval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ReadCluster.h:14,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ReadCluster.h:14,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _Distance = int; _Tp = ClusterNode; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
  253 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from OverlapAlgorithm.h:13,
                 from ReadCluster.h:14,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ClusterNode&, const ClusterNode&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In member function ‘ClusterNodeVector ReadCluster::getOutput() const’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1020:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1020 |       return std::__unique(__first, __last,
      |              ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1021 |       __gnu_cxx::__ops::__iter_comp_iter(__binary_pred));
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/Util.h:12,
                 from ReadCluster.h:13,
                 from ReadCluster.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ReadCluster::run(size_t, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ClusterNode*, std::vector<ClusterNode> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp
LRAlignment.cpp: In function ‘void LRAlignment::removeDuplicateCells(LRAlignment::LRStackEntry*, LRAlignment::LRHash&)’:
LRAlignment.cpp:560:34: warning: left shift count >= width of type [-Wshift-count-overflow]
  560 |                 iter->second = i << 32 | p->G;
      |                                ~~^~~~~
LRAlignment.cpp:566:27: warning: left shift count >= width of type [-Wshift-count-overflow]
  566 |             hash[key] = i << 32 | p->G;
      |                         ~~^~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Tp = LRAlignment::LRHit; _Alloc = std::allocator<LRAlignment::LRHit>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector<LRAlignment::LRHit>::iterator’ changed in GCC 7.1
  721 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LRAlignment::LRCell&}; _Tp = LRAlignment::LRCell; _Alloc = std::allocator<LRAlignment::LRCell>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<LRAlignment::LRCell>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LRAlignment::LRHit&}; _Tp = LRAlignment::LRHit; _Alloc = std::allocator<LRAlignment::LRHit>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<LRAlignment::LRHit>::iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void LRAlignment::saveTerminalHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRAlignment::LRStackEntry*, int, LRAlignment::LRHitVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void LRAlignment::saveAllHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRAlignment::LRStackEntry*, int, LRAlignment::LRHitVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
   79 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1886 |     __final_insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Distance = int; _Tp = LRAlignment::LRHit; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1667 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1929 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1930 |       __comp);
      |       ~~~~~~~                     
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1942 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘int LRAlignment::resolveDuplicateHits(const BWT*, const SampledSuffixArray*, LRAlignment::LRHitVector&, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1982 |    std::__final_insertion_sort(__first, __last, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void LRAlignment::bwaswAlignment(const string&, const BWT*, const SampledSuffixArray*, const LRAlignment::LRParams&, LRAlignment::LRHitVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRCell*, std::vector<LRAlignment::LRCell> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRCell*, std::vector<LRAlignment::LRCell> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRCell*, std::vector<LRAlignment::LRCell> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type ‘std::vector<LRAlignment::LRHit>::iterator’ changed in GCC 7.1
 1665 |    _M_range_insert(__pos, __first, __last,
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
 1666 |      std::__iterator_category(__first));
      |      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type ‘std::vector<LRAlignment::LRHit>::iterator’ changed in GCC 7.1
 1665 |    _M_range_insert(__pos, __first, __last,
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
 1666 |      std::__iterator_category(__first));
      |      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRAlignment::LRHitVector&, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from LRAlignment.h:13,
                 from LRAlignment.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1982 |    std::__final_insertion_sort(__first, __last, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LRAlignment::LRHit*, std::vector<LRAlignment::LRHit> >’ changed in GCC 7.1
 1982 |    std::__final_insertion_sort(__first, __last, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp
KmerOverlaps.cpp:60:12: warning: width of ‘KmerMatch::index’ exceeds its type
   60 |     size_t index:47;
      |            ^~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Thirdparty/multiple_alignment.h:30,
                 from KmerOverlaps.h:13,
                 from KmerOverlaps.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ApproxSeed&}; _Tp = ApproxSeed; _Alloc = std::allocator<ApproxSeed>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ApproxSeed>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ApproxSeed>::iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Thirdparty/multiple_alignment.h:30,
                 from KmerOverlaps.h:13,
                 from KmerOverlaps.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void _approximateSeededMatch(const string&, int, double, int, int, bool, const BWTIndexSet&, SequenceOverlapPairVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ApproxSeed*, std::vector<ApproxSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ApproxSeed*, std::vector<ApproxSeed> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
rm -f libalgorithm.a
ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libalgorithm.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Algorithm'
Making all in StringGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/StringGraph'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp
rm -f libstringgraph.a
ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libstringgraph.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/StringGraph'
Making all in Concurrency
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Concurrency'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp
rm -f libconcurrency.a
ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libconcurrency.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Concurrency'
Making all in SuffixTools
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SuffixTools'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from SuffixArray.h:11,
                 from SuffixArray.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator<SAElem>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SAElem>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from SuffixArray.h:11,
                 from SuffixArray.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void SuffixArray::removeReads(const NumericIDSet&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAElem*, std::vector<SAElem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from STGlobals.h:14,
                 from STCommon.h:11,
                 from InverseSuffixArray.h:12,
                 from InverseSuffixArray.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from STGlobals.h:14,
                 from STCommon.h:11,
                 from InverseSuffixArray.h:12,
                 from InverseSuffixArray.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/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++/10/bits/stl_algo.h:1950:5: 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
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1964:25: 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
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from InverseSuffixArray.h:12,
                 from InverseSuffixArray.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from InverseSuffixArray.h:12,
                 from InverseSuffixArray.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void InverseSuffixArray::validate() const’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from STGlobals.h:14,
                 from STCommon.h:11,
                 from InverseSuffixArray.h:12,
                 from InverseSuffixArray.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: 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
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: 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
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: 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
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp
In file included from ../Util/EncodedString.h:22,
                 from Occurrence.h:13,
                 from RLBWT.h:13,
                 from BWT.h:18,
                 from BWTDiskConstruction.h:19,
                 from BWTDiskConstruction.cpp:12:
../Util/EncodedString.h: In instantiation of ‘void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]’:
../Util/EncodedString.h:43:18:   required from ‘EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]’
/usr/arm-linux-gnueabi/include/c++/10/ext/new_allocator.h:156:4:   required from ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>]’
/usr/arm-linux-gnueabi/include/c++/10/bits/alloc_traits.h:512:17:   required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<EncodedString<DNACodec> >]’
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:115:30:   required from ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >]’
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1204:21:   required from ‘void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; std::vector<_Tp, _Alloc>::value_type = EncodedString<DNACodec>]’
BWTDiskConstruction.cpp:252:56:   required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  236 |             assert(m_capacity = other.m_capacity);
      |                    ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from SuffixArray.h:11,
                 from BWTDiskConstruction.h:18,
                 from BWTDiskConstruction.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MergeItem&}; _Tp = MergeItem; _Alloc = std::allocator<MergeItem>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MergeItem>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from STGlobals.h:13,
                 from STCommon.h:11,
                 from SuffixArray.h:11,
                 from BWTDiskConstruction.h:18,
                 from BWTDiskConstruction.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘MergeVector computeInitialSAIS(const BWTDiskParameters&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MergeItem*, std::vector<MergeItem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘MergeVector computeInitialBCR(const BWTDiskParameters&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MergeItem*, std::vector<MergeItem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void buildBWTDisk(const BWTDiskParameters&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MergeItem*, std::vector<MergeItem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MergeItem*, std::vector<MergeItem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from SAReader.h:12,
                 from SAReader.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator<SAElem>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SAElem>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/Util.h:12,
                 from SAReader.h:12,
                 from SAReader.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void SAReader::readElems(SAElemVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAElem*, std::vector<SAElem> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from RankProcess.h:13,
                 from RankProcess.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/Util.h:12,
                 from RankProcess.h:13,
                 from RankProcess.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘RankResult RankProcess::process(const SequenceWorkItem&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from STGlobals.h:14,
                 from STCommon.h:11,
                 from SAWriter.h:13,
                 from BWTCABauerCoxRosone.h:12,
                 from BWTCABauerCoxRosone.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Distance = int; _Tp = BWTCA::BCRElem; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from STGlobals.h:14,
                 from STCommon.h:11,
                 from SAWriter.h:13,
                 from BWTCABauerCoxRosone.h:12,
                 from BWTCABauerCoxRosone.cpp:9:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1824 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1886 |     __final_insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1667 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1942 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void BWTCA::runBauerCoxRosone(const DNAEncodedStringVector*, const string&, const string&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1982 |    std::__final_insertion_sort(__first, __last, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTCA::BCRElem*, std::vector<BWTCA::BCRElem> >’ changed in GCC 7.1
 1982 |    std::__final_insertion_sort(__first, __last, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp
rm -f libsuffixtools.a
ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libsuffixtools.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/SuffixTools'
Making all in Scaffold
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Scaffold'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Bigraph/GraphCommon.h:13,
                 from ScaffoldLink.h:14,
                 from ScaffoldRecord.h:14,
                 from ScaffoldRecord.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator<ScaffoldLink>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ScaffoldLink>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ScaffoldLink>::iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Bigraph/GraphCommon.h:13,
                 from ScaffoldLink.h:14,
                 from ScaffoldRecord.h:14,
                 from ScaffoldRecord.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ScaffoldRecord::addLink(const ScaffoldLink&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ScaffoldLink*, std::vector<ScaffoldLink> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ScaffoldRecord::parse(const string&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ScaffoldLink*, std::vector<ScaffoldLink> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Bigraph/Bigraph.h:14,
                 from ScaffoldVertex.h:12,
                 from ScaffoldGroup.h:13,
                 from ScaffoldGroup.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LinkVertexPair&}; _Tp = LinkVertexPair; _Alloc = std::allocator<LinkVertexPair>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<LinkVertexPair>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Bigraph/Bigraph.h:14,
                 from ScaffoldVertex.h:12,
                 from ScaffoldGroup.h:13,
                 from ScaffoldGroup.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ScaffoldGroup::addLink(const ScaffoldLink&, ScaffoldVertex*)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LinkVertexPair*, std::vector<LinkVertexPair> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ScaffoldGroup::computeBestOrdering()’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LinkVertexPair*, std::vector<LinkVertexPair> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Bigraph/Bigraph.h:14,
                 from ScaffoldVertex.h:12,
                 from ScaffoldGroup.h:13,
                 from ScaffoldGroup.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator<ScaffoldLink>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ScaffoldLink>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Bigraph/Bigraph.h:14,
                 from ScaffoldVertex.h:12,
                 from ScaffoldGroup.h:13,
                 from ScaffoldGroup.cpp:10:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void ScaffoldGroup::getLinearLinks(LinkVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ScaffoldLink*, std::vector<ScaffoldLink> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ScaffoldLink*, std::vector<ScaffoldLink> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp
rm -f libscaffold.a
ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libscaffold.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Scaffold'
Making all in GraphDiff
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/GraphDiff'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp
DindelUtil.cpp: In function ‘DindelReturnCode DindelUtil::runDindelPairMatePair(const string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)’:
DindelUtil.cpp:65:10: warning: variable ‘has_complex_variant’ set but not used [-Wunused-but-set-variable]
   65 |     bool has_complex_variant = false;
      |          ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from /usr/arm-linux-gnueabi/include/c++/10/queue:61,
                 from GraphCompare.h:19,
                 from DindelUtil.h:14,
                 from DindelUtil.cpp:11:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator<DindelRead>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DindelRead>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator<DindelRead>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelRead*, std::vector<DindelRead> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp
DindelRealignWindow.cpp: In member function ‘void DindelHaplotype::write(std::ostream&) const’:
DindelRealignWindow.cpp:762:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  762 |     for (size_t x=0; x<m_seq.size(); x++)
      |     ^~~
DindelRealignWindow.cpp:763:26: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  763 |         out << m_seq[x]; out << std::endl;
      |                          ^~~
DindelRealignWindow.cpp:764:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  764 |     for (size_t x=0; x<m_refPos.size(); x++)
      |     ^~~
DindelRealignWindow.cpp:765:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  765 |         out << " " << m_refPos[x]-m_refPos[0]; out << std::endl;
      |                                                ^~~
DindelRealignWindow.cpp: In member function ‘void DindelSequenceHash::print() const’:
DindelRealignWindow.cpp:1037:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1037 |         for (std::list<int>::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl;
      |         ^~~
DindelRealignWindow.cpp:1037:115: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1037 |         for (std::list<int>::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl;
      |                                                                                                                   ^~~
DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector<double>&, std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::list<int> >&, const std::vector<std::vector<double> >&)’:
DindelRealignWindow.cpp:2589:12: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2589 |            for (int h1=0;h1<numAH;h1++)
      |            ^~~
DindelRealignWindow.cpp:2600:16: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2600 |                if (DEBUG_CALLINDEL) {
      |                ^~
DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector<DindelMultiHaplotype>&, const std::vector<std::unordered_map<int, double> >&, double, int)’:
DindelRealignWindow.cpp:2743:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2743 |                 for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
      |                 ^~~
DindelRealignWindow.cpp:2743:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2743 |                 for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
      |                                                                                         ^~~
DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector<DindelMultiHaplotype>&, const std::vector<std::unordered_map<int, double> >&, double, int)’:
DindelRealignWindow.cpp:2906:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2906 |             for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
      |             ^~~
DindelRealignWindow.cpp:2906:85: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2906 |             for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
      |                                                                                     ^~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DindelVariant&}; _Tp = DindelVariant; _Alloc = std::allocator<DindelVariant>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DindelVariant>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘std::vector<DindelVariant> WindowFile::getNextWindow()’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelVariant*, std::vector<DindelVariant> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator<VCFRecord>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<VCFRecord>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void DindelRealignWindow::setAddReadsSingleReadMultiSample(int, int, const std::vector<std::vector<double> >&, std::vector<std::unordered_map<int, double> >&, std::vector<double>&, int, int, std::vector<double>&, std::vector<double>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::list<int> >&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator<DindelRealignWindowResult::HaplotypeProperties>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DindelRealignWindowResult::HaplotypeProperties>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator<DindelRealignWindowResult::HaplotypeProperties>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelRealignWindowResult::HaplotypeProperties*, std::vector<DindelRealignWindowResult::HaplotypeProperties> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void DindelRealignWindowResult::Inference::outputAsVCF(const DindelVariant&, const DindelRealignWindowResult&, VCFCollection&, const ReadTable*) const’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<VCFRecord*, std::vector<VCFRecord> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void DindelRealignWindow::computeProjectedMappingQuality()’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:60,
                 from DindelRealignWindow.cpp:24:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h: In 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 DindelVariant&>, std::tuple<>}; _Key = DindelVariant; _Val = std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>; _KeyOfValue = std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >; _Compare = std::less<DindelVariant>; _Alloc = std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
 2460 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/map:61,
                 from DindelRealignWindow.cpp:24:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h: In member function ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector<int>&, const std::vector<std::vector<double> >&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<DindelVariant, std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall>, std::_Select1st<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> >, std::less<DindelVariant>, std::allocator<std::pair<const DindelVariant, DindelRealignWindowResult::GenotypeCall> > >::const_iterator’ changed in GCC 7.1
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelHaplotype}; _Tp = DindelHaplotype; _Alloc = std::allocator<DindelHaplotype>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DindelHaplotype>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void DindelHaplotype::extractVariants()’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelVariant*, std::vector<DindelVariant> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In constructor ‘DindelMultiHaplotype::DindelMultiHaplotype(const std::vector<DindelReferenceMapping>&, const string&, size_t)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelHaplotype*, std::vector<DindelHaplotype> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DindelRead&}; _Tp = DindelRead; _Alloc = std::allocator<DindelRead>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<DindelRead>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/StdAlnTools.h:13,
                 from DindelRealignWindow.cpp:28:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void DindelRealignWindow::showHaplotypeOnlyReadsSingleRead(int, const std::vector<std::vector<double> >&, int, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelRead*, std::vector<DindelRead> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In member function ‘void DindelRealignWindow::showHaplotypeOnlyReadsMatePairs(int, const std::vector<std::vector<double> >&, int, int)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelRead*, std::vector<DindelRead> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DindelRead*, std::vector<DindelRead> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelHMM.o `test -f 'DindelHMM.cpp' || echo './'`DindelHMM.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp
DeBruijnHaplotypeBuilder.cpp: In member function ‘Vertex* DeBruijnHaplotypeBuilder::extendUnambiguously(Vertex*, StringGraph*, EdgeDir, size_t, size_t)’:
DeBruijnHaplotypeBuilder.cpp:227:16: warning: variable ‘ext_count’ set but not used [-Wunused-but-set-variable]
  227 |         size_t ext_count = 0;
      |                ^~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from ../SuffixTools/BWTIndexSet.h:14,
                 from HapgenUtil.h:14,
                 from HapgenUtil.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator<BWTInterval>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BWTInterval>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LocalAlignmentResult&}; _Tp = LocalAlignmentResult; _Alloc = std::allocator<LocalAlignmentResult>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<LocalAlignmentResult>::iterator’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from ../SuffixTools/BWTIndexSet.h:14,
                 from HapgenUtil.h:14,
                 from HapgenUtil.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘LocalAlignmentResultVector HapgenUtil::alignReadsLocally(const string&, const SeqItemVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LocalAlignmentResult*, std::vector<LocalAlignmentResult> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from ../SuffixTools/BWTIndexSet.h:14,
                 from HapgenUtil.h:14,
                 from HapgenUtil.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LocalAlignmentResult}; _Tp = LocalAlignmentResult; _Alloc = std::allocator<LocalAlignmentResult>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<LocalAlignmentResult>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In function ‘bool HapgenUtil::checkAlignmentsAreConsistent(const string&, const StringVector&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LocalAlignmentResult*, std::vector<LocalAlignmentResult> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../SuffixTools/STGlobals.h:13,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from ../SuffixTools/BWTIndexSet.h:14,
                 from HapgenUtil.h:14,
                 from HapgenUtil.cpp:12:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘bool HapgenUtil::extractHaplotypeReads(const StringVector&, const BWTIndexSet&, int, bool, size_t, int64_t, SeqRecordVector*, SeqRecordVector*)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BWTInterval*, std::vector<BWTInterval> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp
rm -f libgraphdiff.a
ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o 
ar: `u' modifier ignored since `D' is the default (see `U')
arm-linux-gnueabi-ranlib libgraphdiff.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/GraphDiff'
Making all in SGA
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SGA'
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp
index.cpp: In function ‘void parseIndexOptions(int, char**)’:
index.cpp:276:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  276 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from ../Util/EncodedString.h:22,
                 from ../SuffixTools/Occurrence.h:13,
                 from ../SuffixTools/RLBWT.h:13,
                 from ../SuffixTools/BWT.h:18,
                 from ../SuffixTools/BWTDiskConstruction.h:19,
                 from index.cpp:18:
../Util/EncodedString.h: In instantiation of ‘void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]’:
../Util/EncodedString.h:43:18:   required from ‘EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]’
/usr/arm-linux-gnueabi/include/c++/10/ext/new_allocator.h:156:4:   required from ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>]’
/usr/arm-linux-gnueabi/include/c++/10/bits/alloc_traits.h:512:17:   required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<EncodedString<DNACodec> >]’
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:115:30:   required from ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >]’
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1204:21:   required from ‘void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; std::vector<_Tp, _Alloc>::value_type = EncodedString<DNACodec>]’
index.cpp:130:45:   required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  236 |             assert(m_capacity = other.m_capacity);
      |                    ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp
overlap.cpp: In function ‘void parseOverlapOptions(int, char**)’:
overlap.cpp:327:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  327 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp
assemble.cpp: In function ‘void parseAssembleOptions(int, char**)’:
assemble.cpp:234:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  234 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp
correct.cpp: In function ‘void parseCorrectOptions(int, char**)’:
correct.cpp:330:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  330 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp
oview.cpp: In function ‘void parseOviewOptions(int, char**)’:
oview.cpp:202:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  202 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp
preprocess.cpp: In function ‘void parsePreprocessOptions(int, char**)’:
preprocess.cpp:616:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  616 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp
rmdup.cpp: In function ‘void parseRmdupOptions(int, char**)’:
rmdup.cpp:348:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  348 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp
merge.cpp: In function ‘void parseMergeOptions(int, char**)’:
merge.cpp:173:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  173 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp
subgraph.cpp: In function ‘void parseSubgraphOptions(int, char**)’:
subgraph.cpp:169:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  169 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp
scaffold.cpp: In function ‘void parseScaffoldOptions(int, char**)’:
scaffold.cpp:189:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  189 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp
scaffold2fasta.cpp: In function ‘void parseScaffold2fastaOptions(int, char**)’:
scaffold2fasta.cpp:196:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  196 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp
connect.cpp: In function ‘void parseConnectOptions(int, char**)’:
connect.cpp:465:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  465 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp
walk.cpp: In function ‘void parseWalkOptions(int, char**)’:
walk.cpp:323:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  323 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp
filter.cpp: In function ‘void parseFilterOptions(int, char**)’:
filter.cpp:217:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  217 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp
kmer-count.cpp: In function ‘void parseKmerCountOptions(int, char**)’:
kmer-count.cpp:63:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
   63 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp
stats.cpp: In function ‘void parseStatsOptions(int, char**)’:
stats.cpp:171:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  171 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp
fm-merge.cpp: In function ‘void parseFMMergeOptions(int, char**)’:
fm-merge.cpp:164:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  164 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp
gmap.cpp: In function ‘void parseGmapOptions(int, char**)’:
gmap.cpp:303:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  303 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp
filterBAM.cpp: In function ‘void parseFilterBAMOptions(int, char**)’:
filterBAM.cpp:438:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  438 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp
cluster.cpp: In function ‘void parseClusterOptions(int, char**)’:
cluster.cpp:292:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  292 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp
gen-ssa.cpp: In function ‘void parseGenSSAOptions(int, char**)’:
gen-ssa.cpp:108:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  108 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp
bwt2fa.cpp: In function ‘void parseBWT2FAOptions(int, char**)’:
bwt2fa.cpp:96:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
   96 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp
graph-diff.cpp: In function ‘void parseGraphDiffOptions(int, char**)’:
graph-diff.cpp:493:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  493 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp
graph-concordance.cpp: In function ‘std::string reconstructHaplotype(const VCFRecord&, VariantRecordVector, const ReadTable&, const BWTIndexSet&, size_t)’:
graph-concordance.cpp:214:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
  214 |     if(end > chr.seq.length())
      |        ~~~~^~~~~~~~~~~~~~~~~~
graph-concordance.cpp: In function ‘void parseGraphConcordanceOptions(int, char**)’:
graph-concordance.cpp:437:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  437 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
gapfill.cpp: In function ‘void parseGapFillOptions(int, char**)’:
gapfill.cpp:148:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  148 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp
In file included from ../Thirdparty/rapidjson/reader.h:7,
                 from ../Thirdparty/rapidjson/document.h:4,
                 from preqc.cpp:27:
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF8<CharType>::TakeBOM(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef170’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:170:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  170 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static rapidjson::UTF8<CharType>::Ch rapidjson::UTF8<CharType>::Take(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef183’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:183:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  183 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8<CharType>::PutBOM(OutputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef189’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:189:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  189 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8<CharType>::Put(OutputByteStream&, rapidjson::UTF8<CharType>::Ch)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef195’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:195:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  195 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16<CharType>::Encode(OutputStream&, unsigned int)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef219’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:219:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  219 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16<CharType>::Decode(InputStream&, unsigned int*)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef234’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:234:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  234 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16<CharType>::Validate(InputStream&, OutputStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef252’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:252:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  252 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef253’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:253:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  253 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE<CharType>::TakeBOM(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef271’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:271:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  271 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE<CharType>::Take(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef278’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:278:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  278 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE<CharType>::PutBOM(OutputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef286’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:286:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  286 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE<CharType>::Put(OutputByteStream&, CharType)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef292’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:292:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  292 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE<CharType>::TakeBOM(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef303’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:303:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  303 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE<CharType>::Take(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef310’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:310:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  310 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE<CharType>::PutBOM(OutputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef318’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:318:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  318 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE<CharType>::Put(OutputByteStream&, CharType)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef324’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:324:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  324 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32<CharType>::Encode(OutputStream&, unsigned int)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef348’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:348:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  348 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32<CharType>::Decode(InputStream&, unsigned int*)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef355’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:355:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  355 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32<CharType>::Validate(InputStream&, OutputStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef363’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:363:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  363 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE<CharType>::TakeBOM(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef375’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:375:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  375 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE<CharType>::Take(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef382’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:382:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  382 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE<CharType>::PutBOM(OutputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef392’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:392:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  392 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE<CharType>::Put(OutputByteStream&, CharType)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef398’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:398:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  398 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE<CharType>::TakeBOM(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef411’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:411:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  411 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE<CharType>::Take(InputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef418’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:418:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  418 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE<CharType>::PutBOM(OutputByteStream&)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef428’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:428:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  428 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE<CharType>::Put(OutputByteStream&, CharType)’:
../Thirdparty/rapidjson/rapidjson.h:115:17: warning: typedef ‘StaticAssertTypedef434’ locally defined but not used [-Wunused-local-typedefs]
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |                 ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’
  111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
      |                                  ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’
  109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
      |                              ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro ‘RAPIDJSON_JOIN’
  115 |  RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
      |  ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:434:3: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’
  434 |   RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
preqc.cpp: In function ‘void parsePreQCOptions(int, char**)’:
preqc.cpp:2090:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
 2090 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/queue:62,
                 from preqc.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from preqc.h:14,
                 from preqc.cpp:16:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from /usr/arm-linux-gnueabi/include/c++/10/queue:61,
                 from preqc.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from /usr/arm-linux-gnueabi/include/c++/10/queue:61,
                 from preqc.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘void generate_gc_distribution(JSONWriter*, const BWTIndexSet&)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from /usr/arm-linux-gnueabi/include/c++/10/queue:61,
                 from preqc.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/RLBWT.h:12,
                 from ../SuffixTools/BWT.h:18,
                 from preqc.h:14,
                 from preqc.cpp:16:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from /usr/arm-linux-gnueabi/include/c++/10/queue:61,
                 from preqc.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
preqc.cpp:1191:13: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
 1191 |     #pragma omp parallel for
      |             ^~~
preqc.cpp:1191:13: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp
overlap-long.cpp: In function ‘void parseOverlapLongOptions(int, char**)’:
overlap-long.cpp:338:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  338 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.cpp
variant-detectability.cpp: In function ‘void parseVarDetectOptions(int, char**)’:
variant-detectability.cpp:205:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  205 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp
rewrite-evidence-bam.cpp: In function ‘void parseRewriteEvidenceBAMOptions(int, char**)’:
rewrite-evidence-bam.cpp:158:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  158 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp
somatic-variant-filters.cpp: In function ‘void parseSomaticVariantFiltersOptions(int, char**)’:
somatic-variant-filters.cpp:794:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
  794 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:61,
                 from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/BWTAlgorithms.h:12,
                 from somatic-variant-filters.cpp:16:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/algorithm:62,
                 from ../SuffixTools/STGlobals.h:14,
                 from ../SuffixTools/STCommon.h:11,
                 from ../SuffixTools/BWTAlgorithms.h:12,
                 from somatic-variant-filters.cpp:16:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1844 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1950 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1964 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h: In function ‘double median(std::vector<T>) [with T = double]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1979 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1980 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1981 |     __comp);
      |     ~~~~~~~              
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1891 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1896 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from somatic-variant-filters.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In function ‘CoverageStats getVariantCoverage(BamTools::BamReader*, const VCFRecord&, const ReadTable*)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp
haplotype-filter.cpp: In function ‘void parseHaplotypeFilterOptions(int, char**)’:
haplotype-filter.cpp:1066:75: warning: comparison is always true due to limited range of data type [-Wtype-limits]
 1066 |     for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:72,
                 from ../Util/Util.h:12,
                 from haplotype-filter.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabi/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabi/include/c++/10/vector:67,
                 from ../Util/Util.h:12,
                 from haplotype-filter.cpp:14:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h: In function ‘std::vector<double> loadSampleDepthsFromFile(std::string)’:
/usr/arm-linux-gnueabi/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp
arm-linux-gnueabi-g++ -Wall -Wextra  -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp  -L/usr//lib -L/usr//lib/bamtools -Wl,-z,relro -Wl,-z,now -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lz  -lbamtools
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/SGA'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh: command-omitted: The call to "dh_auto_test -a -O--sourcedirectory=src" was omitted due to "DEB_BUILD_OPTIONS=nocheck"
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a -O--sourcedirectory=src
   dh_prep -a -O--sourcedirectory=src
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
	cd src && make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/sga AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Making install in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/bin'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/bin'
 /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/sga/usr/bin'
 /usr/bin/install -c sga-bam2de sga-mergeDriver '/<<PKGBUILDDIR>>/debian/sga/usr/bin'
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/bin'
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Making install in Thirdparty
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Thirdparty'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/Thirdparty'
make[4]: Nothing to be done for 'install-exec-am'.
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Making install in Util
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Util'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/Util'
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Making install in SQG
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SQG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/SQG'
make[4]: Nothing to be done for 'install-exec-am'.
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Making install in Bigraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Bigraph'
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Bigraph'
Making install in Algorithm
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Algorithm'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/Algorithm'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/Algorithm'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Algorithm'
Making install in StringGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/StringGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/StringGraph'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/StringGraph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/StringGraph'
Making install in Concurrency
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Concurrency'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/Concurrency'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/Concurrency'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Concurrency'
Making install in SuffixTools
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SuffixTools'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/SuffixTools'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/SuffixTools'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/SuffixTools'
Making install in Scaffold
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/Scaffold'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/Scaffold'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Scaffold'
Making install in GraphDiff
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/GraphDiff'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/GraphDiff'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/GraphDiff'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/GraphDiff'
Making install in SGA
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/SGA'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/SGA'
 /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/sga/usr/bin'
  /usr/bin/install -c sga '/<<PKGBUILDDIR>>/debian/sga/usr/bin'
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/SGA'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/SGA'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cp -a src/bin/sga-bam2de.pl	debian/sga/usr/bin/sga-bam2de
cp -a src/bin/sga-astat.py	debian/sga/usr/bin/sga-astat
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a -O--sourcedirectory=src
   dh_installdocs -a -O--sourcedirectory=src
   dh_installchangelogs -a -O--sourcedirectory=src
   debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
mkdir -p debian/sga/usr/share/doc/sga/examples
sed -e 's?^\(SGA_BIN=sga\).*?\1?' \
    -e 's?^.*/bin/sga-align?sga-align?' \
    -e 's?^.*/bin/sga-bam2de.pl?sga-bam2de?' \
    -e 's?^.*/bin/sga-astat.py?sga-astat?' \
    src/examples/sga-celegans.sh > debian/sga/usr/share/doc/sga/examples/sga-celegans.sh
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
mkdir -p /<<PKGBUILDDIR>>/debian/sga/usr/share/man/man1/
PATH=/usr/lib/abyss:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \
help2man \
	--version-string="0.10.15" \
	--no-info \
	--name "Make a distance estimate file from a bam file of reads aligned to contigs" \
	--output /<<PKGBUILDDIR>>/debian/sga/usr/share/man/man1//sga-bam2de.1 \
	/<<PKGBUILDDIR>>/debian/sga/usr/bin/sga-bam2de
help2man \
	--no-info \
	--version-string="0.10.15" \
	--name="String Graph Assembler: de novo genome assembler that uses string graphs" \
	--output /<<PKGBUILDDIR>>/debian/sga/usr/share/man/man1//sga.1 \
	/<<PKGBUILDDIR>>/debian/sga/usr/bin/sga
help2man: can't get `--help' info from /<<PKGBUILDDIR>>/debian/sga/usr/bin/sga
Try `--no-discard-stderr' if option outputs to stderr
make[1]: *** [debian/rules:38: override_dh_installman] Error 126
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2021-10-03T10:36:55Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 335124
Build-Time: 319
Distribution: unstable
Fail-Stage: build
Foreign Architectures: armel
Host Architecture: armel
Install-Time: 38
Job: sga_0.10.15-7
Machine Architecture: amd64
Package: sga
Package-Time: 368
Source-Version: 0.10.15-7
Space: 335124
Status: attempted
Version: 0.10.15-7
--------------------------------------------------------------------------------
Finished at 2021-10-03T10:36:55Z
Build needed 00:06:08, 335124k disk space