sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | progressivemauve 1.2.0+4713+dfsg-4 (armhf) Thu, 30 May 2019 13:12:11 +0000 | +==============================================================================+ Package: progressivemauve Version: 1.2.0+4713+dfsg-4 Source Version: 1.2.0+4713+dfsg-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-41a79a26-3675-404d-a4f5-5e2bfbd376ea' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [247 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-30-0819.31.pdiff [1341 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-30-0819.31.pdiff [466 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-30-0819.31.pdiff [1341 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-30-0819.31.pdiff [466 B] Get:6 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8083 kB] Fetched 8388 kB in 2s (4270 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'progressivemauve' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/progressivemauve.git Please use: git clone https://salsa.debian.org/med-team/progressivemauve.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 116 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (dsc) [2300 B] Get:2 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (tar) [96.1 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main progressivemauve 1.2.0+4713+dfsg-4 (diff) [17.7 kB] Fetched 116 kB in 0s (0 B/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/progressivemauve-jXjO9Y/progressivemauve-1.2.0+4713+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/progressivemauve-jXjO9Y' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-8z9EQF/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-8z9EQF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8z9EQF/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-8z9EQF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8z9EQF/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-8z9EQF/apt_archive ./ Packages [453 B] Fetched 1773 B in 0s (97.1 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libmpx2-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev autoconf automake libtool flex bison gdb-arm-linux-gnueabihf gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sbuild-build-depends-core-dummy:armhf sensible-utils ucf 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 41.8 MB of archives. After this operation, 152 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8z9EQF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.31.1-16 [2834 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf-base amd64 8.3.0-7cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [6545 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.28-10cross2 [1172 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:8.3.0-7cross1 [37.1 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 8.3.0-7cross1 [63.2 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 8.3.0-7cross1 [6564 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 8.3.0-7cross1 [301 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 8.3.0-7cross1 [329 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 8.3.0-7cross1 [103 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-armhf-cross all 8.3.0-7cross1 [612 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [6973 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:8.3.0-1 [1456 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 4.19.28-2cross2 [1228 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.28-10cross2 [2149 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-armhf-cross all 8.3.0-7cross1 [1556 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [7126 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:8.3.0-1 [1180 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.8 MB in 1s (62.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11953 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Setting up gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-7cross1) ... Setting up linux-libc-dev-armhf-cross (4.19.28-2cross2) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-16) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up libgomp1-armhf-cross (8.3.0-7cross1) ... Setting up libc6-dev-armhf-cross (2.28-10cross2) ... Setting up libstdc++6-armhf-cross (8.3.0-7cross1) ... Setting up libubsan1-armhf-cross (8.3.0-7cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up cpp-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan5-armhf-cross (8.3.0-7cross1) ... Setting up libgcc-8-dev-armhf-cross (8.3.0-7cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-armhf-cross (8.3.0-7cross1) ... Setting up gcc-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up gcc-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up g++-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.6) ... Setting up sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-8z9EQF/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-8z9EQF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8z9EQF/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-8z9EQF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8z9EQF/apt_archive ./ Sources [485 B] Get:5 copy:/<>/resolver-8z9EQF/apt_archive ./ Packages [570 B] Fetched 2018 B in 0s (105 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:armhf 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-8z9EQF/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:armhf. (Reading database ... 15002 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev dpkg-deb: building package 'sbuild-build-depends-progressivemauve-dummy' in '/<>/resolver-8z9EQF/apt_archive/sbuild-build-depends-progressivemauve-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-progressivemauve-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-8z9EQF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8z9EQF/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-8z9EQF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8z9EQF/apt_archive ./ Sources [705 B] Get:5 copy:/<>/resolver-8z9EQF/apt_archive ./ Packages [780 B] Fetched 2448 B in 0s (118 kB/s) Reading package lists... Reading package lists... Install progressivemauve build dependencies (apt-based resolver) ---------------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libboost-dev:armhf libboost-filesystem-dev:armhf libboost-filesystem1.67-dev:armhf libboost-filesystem1.67.0:armhf libboost-iostreams-dev:armhf libboost-iostreams1.67-dev:armhf libboost-iostreams1.67.0:armhf libboost-program-options-dev:armhf libboost-program-options1.67-dev:armhf libboost-program-options1.67.0:armhf libboost-regex1.67-dev:armhf libboost-regex1.67.0:armhf libboost-system-dev:armhf libboost-system1.67-dev:armhf libboost-system1.67.0:armhf libboost1.67-dev:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgenome-dev:armhf libgenome0:armhf libglib2.0-0 libgomp1:armhf libicu-dev:armhf libicu63:armhf libmems-dev:armhf libmems1:armhf libmuscle-dev:armhf libmuscle1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db pkgconf po-debconf zlib1g:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:armhf libboost1.67-doc:armhf libboost-atomic1.67-dev:armhf libboost-chrono1.67-dev:armhf libboost-container1.67-dev:armhf libboost-context1.67-dev:armhf libboost-coroutine1.67-dev:armhf libboost-date-time1.67-dev:armhf libboost-exception1.67-dev:armhf libboost-fiber1.67-dev:armhf libboost-graph1.67-dev:armhf libboost-graph-parallel1.67-dev:armhf libboost-locale1.67-dev:armhf libboost-log1.67-dev:armhf libboost-math1.67-dev:armhf libboost-mpi1.67-dev:armhf libboost-mpi-python1.67-dev:armhf libboost-numpy1.67-dev:armhf libboost-python1.67-dev:armhf libboost-random1.67-dev:armhf libboost-serialization1.67-dev:armhf libboost-signals1.67-dev:armhf libboost-stacktrace1.67-dev:armhf libboost-test1.67-dev:armhf libboost-thread1.67-dev:armhf libboost-timer1.67-dev:armhf libboost-type-erasure1.67-dev:armhf libboost-wave1.67-dev:armhf libboost1.67-tools-dev:armhf libmpfrc++-dev:armhf libntl-dev:armhf glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf icu-doc:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libboost-dev:armhf libboost-filesystem-dev:armhf libboost-filesystem1.67-dev:armhf libboost-filesystem1.67.0:armhf libboost-iostreams-dev:armhf libboost-iostreams1.67-dev:armhf libboost-iostreams1.67.0:armhf libboost-program-options-dev:armhf libboost-program-options1.67-dev:armhf libboost-program-options1.67.0:armhf libboost-regex1.67-dev:armhf libboost-regex1.67.0:armhf libboost-system-dev:armhf libboost-system1.67-dev:armhf libboost-system1.67.0:armhf libboost1.67-dev:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgenome-dev:armhf libgenome0:armhf libglib2.0-0 libgomp1:armhf libicu-dev:armhf libicu63:armhf libmems-dev:armhf libmems1:armhf libmuscle-dev:armhf libmuscle1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db pkgconf po-debconf sbuild-build-depends-progressivemauve-dummy:armhf zlib1g:armhf 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 49.5 MB of archives. After this operation, 316 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8z9EQF/apt_archive ./ sbuild-build-depends-progressivemauve-dummy 0.invalid.0 [932 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-1 [1258 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main armhf gcc-8-base armhf 8.3.0-7 [191 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 icu-devtools amd64 63.1-6 [188 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:8.3.0-7 [37.1 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.28-10 [2390 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 8.3.0-7 [339 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 8.3.0-7 [336 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 8.3.0-7 [6740 B] Get:36 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 8.3.0-7 [64.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 8.3.0-7 [103 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-8-dev armhf 8.3.0-7 [611 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 4.19.37-3 [1166 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.28-10 [2149 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-8-dev armhf 8.3.0-7 [1585 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main armhf libboost-dev armhf 1.67.0.1 [3860 B] Get:44 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.67.0 armhf 1.67.0-13 [228 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.67.0 armhf 1.67.0-13 [255 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.67-dev armhf 1.67.0-13 [232 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.67-dev armhf 1.67.0-13 [262 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem-dev armhf 1.67.0.1 [3684 B] Get:49 http://debian.oregonstate.edu/debian unstable/main armhf libicu63 armhf 63.1-6 [8000 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main armhf libboost-regex1.67.0 armhf 1.67.0-13 [437 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main armhf libicu-dev armhf 63.1-6 [8934 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main armhf libboost-regex1.67-dev armhf 1.67.0-13 [539 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main armhf libbz2-1.0 armhf 1.0.6-9 [43.6 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.9 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams1.67.0 armhf 1.67.0-13 [245 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13 [254 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams-dev armhf 1.67.0.1 [3632 B] Get:58 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.67.0 armhf 1.67.0-13 [334 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.67-dev armhf 1.67.0-13 [384 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options-dev armhf 1.67.0.1 [3656 B] Get:61 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system-dev armhf 1.67.0.1 [3788 B] Get:62 http://debian.oregonstate.edu/debian unstable/main armhf libgenome0 armhf 1.3.11+svn20110227.4616-2 [98.1 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main armhf libgenome-dev armhf 1.3.11+svn20110227.4616-2 [174 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main armhf libmuscle1 armhf 3.7+4565-6 [202 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main armhf libmems1 armhf 1.6.0+4725-8+b1 [516 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main armhf libmuscle-dev armhf 3.7+4565-6 [256 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main armhf libmems-dev armhf 1.6.0+4725-8+b1 [808 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 pkgconf amd64 1.6.0-1 [66.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.5 MB in 1s (63.8 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15002 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package gettext-base. 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Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by pkgconf' Adding 'diversion of /usr/share/aclocal/pkg.m4 to /usr/share/aclocal/pkg.real.m4 by pkgconf' Adding 'diversion of /usr/share/man/man1/pkg-config.1.gz to /usr/share/man/man1/pkg-config.real.1.gz by pkgconf' Adding 'diversion of /usr/share/pkg-config-crosswrapper to /usr/share/pkg-config-crosswrapper.real by pkgconf' Unpacking pkgconf (1.6.0-1) ... Selecting previously unselected package sbuild-build-depends-progressivemauve-dummy:armhf. Preparing to unpack .../67-sbuild-build-depends-progressivemauve-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-progressivemauve-dummy:armhf (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up linux-libc-dev:armhf (4.19.37-3) ... Setting up gettext-base (0.19.8.1-9) ... Setting up pkgconf (1.6.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:armhf (8.3.0-7) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up icu-devtools (63.1-6) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:armhf (2.28-10) ... Setting up libc6-dev:armhf (2.28-10) ... Setting up libbz2-1.0:armhf (1.0.6-9) ... Setting up libgcc1:armhf (1:8.3.0-7) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ... Setting up libgomp1:armhf (8.3.0-7) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:armhf (8.3.0-7) ... Setting up libstdc++6:armhf (8.3.0-7) ... Setting up libboost-program-options1.67.0:armhf (1.67.0-13) ... Setting up libgenome0:armhf (1.3.11+svn20110227.4616-2) ... Setting up libmuscle1:armhf (3.7+4565-6) ... Setting up libgenome-dev:armhf (1.3.11+svn20110227.4616-2) ... Setting up debhelper (12.1.1) ... Setting up libicu63:armhf (63.1-6) ... Setting up libasan5:armhf (8.3.0-7) ... Setting up libmuscle-dev:armhf (3.7+4565-6) ... Setting up libboost-iostreams1.67.0:armhf (1.67.0-13) ... Setting up libubsan1:armhf (8.3.0-7) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libboost-system1.67.0:armhf (1.67.0-13) ... Setting up libicu-dev:armhf (63.1-6) ... Setting up libboost-regex1.67.0:armhf (1.67.0-13) ... Setting up libgcc-8-dev:armhf (8.3.0-7) ... Setting up libboost-filesystem1.67.0:armhf (1.67.0-13) ... Setting up libstdc++-8-dev:armhf (8.3.0-7) ... Setting up libboost1.67-dev:armhf (1.67.0-13) ... Setting up libboost-program-options1.67-dev:armhf (1.67.0-13) ... Setting up libboost-regex1.67-dev:armhf (1.67.0-13) ... Setting up libmems1:armhf (1.6.0+4725-8+b1) ... Setting up libboost-program-options-dev:armhf (1.67.0.1) ... Setting up libboost-system1.67-dev:armhf (1.67.0-13) ... Setting up libboost-dev:armhf (1.67.0.1) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13) ... Setting up libboost-filesystem1.67-dev:armhf (1.67.0-13) ... Setting up libboost-system-dev:armhf (1.67.0.1) ... Setting up libmems-dev:armhf (1.6.0+4725-8+b1) ... Setting up libboost-iostreams-dev:armhf (1.67.0.1) ... Setting up libboost-filesystem-dev:armhf (1.67.0.1) ... Setting up sbuild-build-depends-progressivemauve-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.6 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armhf-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armhf-cross_8.3.0-7cross1 linux-libc-dev_4.19.37-3 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-arm-linux-gnueabihf_2.31.1-16 binutils-common_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-7 cpp-8-arm-linux-gnueabihf_8.3.0-7cross1 cpp-arm-linux-gnueabihf_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.6 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.6 dpkg-cross_2.6.15-3 dpkg-dev_1.19.6 dwz_0.12-3 e2fsprogs_1.45.1-3 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1 g++-8_8.3.0-7 g++-8-arm-linux-gnueabihf_8.3.0-7cross1 g++-arm-linux-gnueabihf_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-7 gcc-8-arm-linux-gnueabihf_8.3.0-7cross1 gcc-8-arm-linux-gnueabihf-base_8.3.0-7cross1 gcc-8-base_8.3.0-7 gcc-8-cross-base_8.3.0-7cross1 gcc-arm-linux-gnueabihf_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-2 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 icu-devtools_63.1-6 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-7 libasan5-armhf-cross_8.3.0-7cross1 libatomic1_8.3.0-7 libatomic1-armhf-cross_8.3.0-7cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1 libboost-filesystem-dev_1.67.0.1 libboost-filesystem1.67-dev_1.67.0-13 libboost-filesystem1.67.0_1.67.0-13 libboost-iostreams-dev_1.67.0.1 libboost-iostreams1.67-dev_1.67.0-13 libboost-iostreams1.67.0_1.67.0-13 libboost-program-options-dev_1.67.0.1 libboost-program-options1.67-dev_1.67.0-13 libboost-program-options1.67.0_1.67.0-13 libboost-regex1.67-dev_1.67.0-13 libboost-regex1.67.0_1.67.0-13 libboost-system-dev_1.67.0.1 libboost-system1.67-dev_1.67.0-13 libboost-system1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-armhf-cross_2.28-10cross2 libc6-dev_2.28-10 libc6-dev-armhf-cross_2.28-10cross2 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-7 libcom-err2_1.45.1-3 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.6 libelf1_0.176-1.1 libext2fs2_1.45.1-3 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-7 libgcc-8-dev-armhf-cross_8.3.0-7cross1 libgcc1_1:8.3.0-7 libgcc1-armhf-cross_1:8.3.0-7cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgenome-dev_1.3.11+svn20110227.4616-2 libgenome0_1.3.11+svn20110227.4616-2 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-3 libgomp1_8.3.0-7 libgomp1-armhf-cross_8.3.0-7cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu-dev_63.1-6 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-7 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-7 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmems-dev_1.6.0+4725-8+b1 libmems1_1.6.0+4725-8+b1 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-7 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_8.3.0-7 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.1-3 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armhf-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armhf-cross_8.3.0-7cross1 libsystemd0_241-5 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libubsan1-armhf-cross_8.3.0-7cross1 libuchardet0_0.0.6-3 libudev1_241-5 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-3 linux-libc-dev-armhf-cross_4.19.28-2cross2 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pkgconf_1.6.0-1 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-progressivemauve-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Dec 4 09:10:58 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./progressivemauve_1.2.0+4713+dfsg-4.dsc dpkg-source: info: extracting progressivemauve in /<>/progressivemauve-1.2.0+4713+dfsg dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg.orig.tar.xz dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build.patch dpkg-source: info: applying do_not_build_static_binaries.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying use-native-getopt.patch dpkg-source: info: applying adapt-to-unversioned-libs.patch dpkg-source: info: applying fix_FTBFS_boost1.67.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-41a79a26-3675-404d-a4f5-5e2bfbd376ea SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package progressivemauve dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf 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 armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:21: installing 'config/compile' configure.ac:9: installing 'config/config.guess' configure.ac:9: installing 'config/config.sub' configure.ac:11: installing 'config/install-sh' configure.ac:11: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/Makefile.am: installing 'config/depcomp' src/Makefile.am:51: warning: variable 'EXTRA_mauveStatic_SOURCES' is defined but no program or src/Makefile.am:51: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:49: warning: variable 'mauveStatic_SOURCES' is defined but no program or src/Makefile.am:49: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:160: warning: variable 'progressiveMauveStatic_SOURCES' is defined but no program or src/Makefile.am:160: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:50: warning: variable 'mauveStatic_LDADD' is defined but no program or src/Makefile.am:50: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:161: warning: variable 'progressiveMauveStatic_LDADD' is defined but no program or src/Makefile.am:161: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:52: warning: variable 'mauveStatic_DEPENDENCIES' is defined but no program or src/Makefile.am:52: library has 'mauveStatic' as canonical name (possible typo) dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabihf configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armhf checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabihf-strip... arm-linux-gnueabihf-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for arm-linux-gnueabihf-gcc... arm-linux-gnueabihf-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabihf-gcc accepts -g... yes checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabihf-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabihf-gcc... none checking for arm-linux-gnueabihf-g++... arm-linux-gnueabihf-g++ checking whether we are using the GNU C++ compiler... yes checking whether arm-linux-gnueabihf-g++ accepts -g... yes checking dependency style of arm-linux-gnueabihf-g++... none checking whether ln -s works... yes checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for getopt_long... yes checking for getopt... yes checking for arm-linux-gnueabihf-pkg-config... /usr/bin/arm-linux-gnueabihf-pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking for memset... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... yes checking whether arm-linux-gnueabihf-gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg' Making all in src make[2]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make all-am make[3]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveAligner.o mauveAligner.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from mauveAligner.cpp:30: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/MatchFinder.h:17, from /usr/include/libMems/MemHash.h:20, from mauveAligner.cpp:22: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Match.h:20, from /usr/include/libMems/MatchFinder.h:17, from /usr/include/libMems/MemHash.h:20, from mauveAligner.cpp:22: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from mauveAligner.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wl,-z,relro -Wl,-z,now -o mauveAligner mauveAligner.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scoreAlignment.o scoreAlignment.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'virtual void VectorIntervalMap::add(gnSeqI, gnSeqI)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/MatchList.h:22, from scoreAlignment.cpp:13: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Match.h:20, from /usr/include/libMems/MatchList.h:22, from scoreAlignment.cpp:13: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqueMerCount.o uniqueMerCount.cpp arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toRawSequence.o toRawSequence.cpp arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mfa2xmfa.o mfa2xmfa.cpp arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mfa2xmfa mfa2xmfa.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o addUnalignedIntervals.o addUnalignedIntervals.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from addUnalignedIntervals.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from addUnalignedIntervals.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from addUnalignedIntervals.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o addUnalignedIntervals addUnalignedIntervals.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toMultiFastA.o toMultiFastA.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from toMultiFastA.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from toMultiFastA.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from toMultiFastA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getAlignmentWindows.o getAlignmentWindows.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getAlignmentWindows.cpp:14: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from getAlignmentWindows.cpp:13: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from getAlignmentWindows.cpp:13: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getAlignmentWindows getAlignmentWindows.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniquifyTrees.o uniquifyTrees.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/PhyloTree.h:8, from uniquifyTrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/PhyloTree.h:8, from uniquifyTrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree::readTree(std::istream&) [with T = TreeNode]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniquifyTrees uniquifyTrees.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toGrimmFormat.o toGrimmFormat.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from toGrimmFormat.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from toGrimmFormat.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toGrimmFormat toGrimmFormat.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from mauveToXMFA.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from mauveToXMFA.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mauveToXMFA mauveToXMFA.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripGapColumns.o stripGapColumns.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from stripGapColumns.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from stripGapColumns.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripGapColumns stripGapColumns.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from progressiveMauve.cpp:26: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ progressiveMauve.cpp:417:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ progressiveMauve.cpp:417:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/MatchFinder.h:17, from /usr/include/libMems/MemHash.h:20, from progressiveMauve.cpp:21: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void applyBackbone(mems::IntervalList&, std::__cxx11::string&, std::__cxx11::string&, size_t, double, double, double)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Match.h:20, from /usr/include/libMems/MatchFinder.h:17, from /usr/include/libMems/MemHash.h:20, from progressiveMauve.cpp:21: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/Matrix.h:19, from progressiveMauve.cpp:17: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UniqueMatchFinder.o UniqueMatchFinder.cpp arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/PhyloTree.h:8, from extractBCITrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' {aka '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair, std::allocator >, double>&}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' {aka '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/PhyloTree.h:8, from extractBCITrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree::readTree(std::istream&) [with T = TreeNode]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from extractBCITrees.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double>*, std::vector, double> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from extractBCITrees.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/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 = std::pair, double>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, double>*, std::vector, double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from extractBCITrees.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/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-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/PhyloTree.h:8, from extractBCITrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from extractBCITrees.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/PhyloTree.h:8, from extractBCITrees.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o createBackboneMFA.o createBackboneMFA.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from createBackboneMFA.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from createBackboneMFA.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libMems/AbstractMatch.h:17, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from createBackboneMFA.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o repeatoire.o repeatoire.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from repeatoire.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from repeatoire.cpp:2: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GappedMatchRecord&}; _Tp = GappedMatchRecord; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'void writeXmfa(mems::MatchList&, std::vector&, const string&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'void writeXML(mems::MatchList&, std::vector&, const string&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Distance = int; _Tp = std::pair >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from repeatoire.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from repeatoire.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from alignmentProjector.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from alignmentProjector.cpp:11: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from alignmentProjector.cpp:11: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from alignmentProjector.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from alignmentProjector.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const boost::tuples::tuple >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>&}; _Tp = boost::tuples::tuple >; _Alloc = std::allocator > >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector > >::iterator' {aka '__gnu_cxx::__normal_iterator >*, std::vector > > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from stripSubsetLCBs.cpp:12: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from stripSubsetLCBs.cpp:12: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from stripSubsetLCBs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from projectAndStrip.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from projectAndStrip.cpp:12: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from projectAndStrip.cpp:12: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from projectAndStrip.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from projectAndStrip.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from projectAndStrip.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from projectAndStrip.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from makeBadgerMatrix.cpp:10: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from makeBadgerMatrix.cpp:10: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from makeBadgerMatrix.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from randomGeneSample.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from randomGeneSample.cpp:12: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from randomGeneSample.cpp:12: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from randomGeneSample.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getOrthologList.cpp:18: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from getOrthologList.cpp:12: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from getOrthologList.cpp:12: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from getOrthologList.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from getOrthologList.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from getOrthologList.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from getOrthologList.cpp:7: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from getOrthologList.cpp:8: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbFilter.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbFilter.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator > > >}; _Tp = std::pair > >; _Alloc = std::allocator > > >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector > > >::iterator' {aka '__gnu_cxx::__normal_iterator > >*, std::vector > > > >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {genome::gnLocation}; _Tp = genome::gnLocation; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneColsFile(std::istream&, std::vector > > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >*, std::vector > > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const TreeNode&}; _Tp = TreeNode; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = TreeNode; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::tuples::tuple, std::allocator >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>}; _Tp = boost::tuples::tuple >; _Alloc = std::allocator > >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector > >::iterator' {aka '__gnu_cxx::__normal_iterator >*, std::vector > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/set:60, from /usr/include/libMems/Match.h:18, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void PhyloTree::readTree(std::istream&) [with T = TreeNode]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Distance = int; _Tp = boost::tuples::tuple >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mfAnalyze(std::ofstream&, multifun_map_t&, multifun_map_t&, multifun_names_t&, double)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = genome::gnLocation; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void identifyIntergenicRanges(std::vector&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /usr/include/libMems/AbstractMatch.h:18, from /usr/include/libMems/SparseAbstractMatch.h:18, from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/map:61, from /usr/include/libMems/MemHash.h:17, from /usr/include/libMems/IntervalList.h:23, from /usr/include/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_map.h: In function 'void makeMultiFunCount(genome::gnSequence*, multifun_map_t&, multifun_names_t&, mems::bitset_t&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from backbone_global_to_local.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from backbone_global_to_local.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In function 'void mems::readBackboneSeqFile(std::istream&, std::vector > >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from backbone_global_to_local.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from backbone_global_to_local.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from xmfa2maf.cpp:2: /usr/arm-linux-gnueabihf/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from xmfa2maf.cpp:1: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from xmfa2maf.cpp:1: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from xmfa2maf.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/libMems/Match.h:22, from /usr/include/libMems/Interval.h:21, from /usr/include/libMems/IntervalList.h:22, from coordinateTranslate.cpp:5: /usr/include/libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/libMems/Interval.h:18, from /usr/include/libMems/IntervalList.h:22, from coordinateTranslate.cpp:5: /usr/include/libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from /usr/include/libMems/SortedMerList.h:19, from /usr/include/libMems/IntervalList.h:20, from coordinateTranslate.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval<>]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/<>/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -L/usr/lib/arm-linux-gnueabihf -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE make[3]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg' Making install in src make[2]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' /bin/mkdir -p '/<>/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' /usr/bin/install -c mauveAligner scoreAlignment uniqueMerCount toRawSequence mfa2xmfa addUnalignedIntervals toMultiFastA getAlignmentWindows uniquifyTrees toGrimmFormat mauveToXMFA stripGapColumns progressiveMauve extractBCITrees createBackboneMFA repeatoire alignmentProjector stripSubsetLCBs projectAndStrip makeBadgerMatrix randomGeneSample getOrthologList bbFilter bbAnalyze backbone_global_to_local xmfa2maf coordinateTranslate '/<>/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[3]: Entering directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[2]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/<>/progressivemauve-1.2.0+4713+dfsg' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/projectAndStrip contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/createBackboneMFA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/uniqueMerCount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/randomGeneSample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toGrimmFormat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/stripGapColumns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/makeBadgerMatrix contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mfa2xmfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/scoreAlignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/progressiveMauve contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/bbFilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/xmfa2maf contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/extractBCITrees contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/bbAnalyze contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/getAlignmentWindows contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toMultiFastA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/addUnalignedIntervals contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mauveAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/mauveToXMFA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/stripSubsetLCBs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/backbone_global_to_local contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/coordinateTranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/getOrthologList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/uniquifyTrees contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/repeatoire contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/alignmentProjector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/progressivemauve/usr/bin/toRawSequence contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/toRawSequence were not linked against libMUSCLE.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/toRawSequence were not linked against librt.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/toRawSequence were not linked against libboost_system.so.1.67.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/stripSubsetLCBs debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/toRawSequence were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-4_armhf.deb'. dpkg-deb: building package 'progressivemauve-dbgsym' in '../progressivemauve-dbgsym_1.2.0+4713+dfsg-4_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../progressivemauve_1.2.0+4713+dfsg-4_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-05-30T13:18:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-8z9EQF/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-progressivemauve-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-8z9EQF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8z9EQF/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-8z9EQF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8z9EQF/apt_archive ./ Sources [822 B] Get:5 copy:/<>/resolver-8z9EQF/apt_archive ./ Packages [900 B] Fetched 2685 B in 0s (148 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libhtml-template-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 7768 kB of archives. After this operation, 20.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8z9EQF/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 7.0-5 [70.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.13-2 [512 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-2 [640 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-2 [866 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1b-2 [1530 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.15.0 [1181 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7768 kB in 0s (39.8 MB/s) Selecting previously unselected package netbase. (Reading database ... 32760 files and directories currently installed.) Preparing to unpack .../00-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package readline-common. Preparing to unpack .../01-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.2-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.2-1) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../04-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.13-2_amd64.deb ... Unpacking gpgconf (2.2.13-2) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.27.2-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-2) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.13-2_amd64.deb ... Unpacking gpg (2.2.13-2) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.34+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.34+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../09-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../10-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../11-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. 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Preparing to unpack .../46-lintian_2.15.0_all.deb ... Unpacking lintian (2.15.0) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:armhf. Preparing to unpack .../47-sbuild-build-depends-lintian-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.34+b1) ... Setting up libstruct-dumb-perl (0.09-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libssl1.1:amd64 (1.1.1b-2) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libsqlite3-0:amd64 (3.27.2-2) ... Setting up libfuture-perl (0.39-1) ... Setting up libyaml-libyaml-perl (0.76+repack-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libio-async-perl (0.72-1) ... Setting up patchutils (0.3.4-2) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up diffstat (1.62-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up netbase (5.6) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (7.0-5) ... Setting up liburi-perl (1.76-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libnet-dns-perl (1.19-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.13-2) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up gpg (2.2.13-2) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmailtools-perl (2.18-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up lintian (2.15.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.28-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ progressivemauve_1.2.0+4713+dfsg-4_armhf.changes: ------------------------------------------------- Format: 1.8 Date: Tue, 04 Dec 2018 10:03:31 +0100 Source: progressivemauve Binary: progressivemauve progressivemauve-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.2.0+4713+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: progressivemauve - multiple genome alignment algorithms Closes: 914049 Changes: progressivemauve (1.2.0+4713+dfsg-4) unstable; urgency=medium . [ Giovanni Mascellani ] * Fix FTBFS with boost1.67 Closes: #914049 . 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progressivemauve_1.2.0+4713+dfsg-4_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 30 May 2019 13:18:20 +0000 Build-Path: /<>/progressivemauve-1.2.0+4713+dfsg Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 10.3), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.31.1-16), binutils-common (= 2.31.1-16), binutils-x86-64-linux-gnu (= 2.31.1-16), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.33.1-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-7), dash (= 0.5.10.2-5), debconf (= 1.5.72), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.6), dpkg-dev (= 1.19.6), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-4), findutils (= 4.6.0+git+20190209-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-7), gcc (= 4:8.3.0-1), gcc-8 (= 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libmagic-mgc (= 1:5.35-4), libmagic1 (= 1:5.35-4), libmems-dev (= 1.6.0+4725-8+b1), libmems1 (= 1.6.0+4725-8+b1), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-7), libmuscle-dev (= 3.7+4565-6), libmuscle1 (= 3.7+4565-6), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre3 (= 2:8.39-12), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libquadmath0 (= 8.3.0-7), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.33.1-0.1), libstdc++-8-dev (= 8.3.0-7), libstdc++6 (= 8.3.0-7), libsystemd0 (= 241-5), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-7), libubsan1 (= 8.3.0-7), libuchardet0 (= 0.0.6-3), libudev1 (= 241-5), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 4.19.37-3), login (= 1:4.5-1.1), m4 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./usr/share/doc/progressivemauve-dbgsym -> progressivemauve progressivemauve_1.2.0+4713+dfsg-4_armhf.deb -------------------------------------------- new Debian package, version 2.0. size 637736 bytes: control archive=2496 bytes. 1927 bytes, 36 lines control 2744 bytes, 42 lines md5sums Package: progressivemauve Version: 1.2.0+4713+dfsg-4 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2801 Depends: libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgenome0, libmems1, libmuscle1 (>= 3.7+4565), libstdc++6 (>= 5.2) Enhances: mauve-aligner Section: science Priority: optional Homepage: http://darlinglab.org/mauve/user-guide/mauvealigner.html Description: multiple genome alignment algorithms The mauveAligner and progressiveMauve alignment algorithms have been implemented as command-line programs included with the downloadable Mauve software. When run from the command-line, these programs provide options not yet available in the graphical interface. . Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. . Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. . Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutition. . Mauve is developed at the University of Wisconsin. drwxr-xr-x root/root 0 2018-12-04 09:03 ./ drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/ drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/bin/ -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/addUnalignedIntervals -rwxr-xr-x root/root 136716 2018-12-04 09:03 ./usr/bin/alignmentProjector -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/backbone_global_to_local -rwxr-xr-x root/root 226844 2018-12-04 09:03 ./usr/bin/bbAnalyze -rwxr-xr-x root/root 38360 2018-12-04 09:03 ./usr/bin/bbFilter -rwxr-xr-x root/root 83468 2018-12-04 09:03 ./usr/bin/coordinateTranslate -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/createBackboneMFA -rwxr-xr-x root/root 62936 2018-12-04 09:03 ./usr/bin/extractBCITrees -rwxr-xr-x root/root 103948 2018-12-04 09:03 ./usr/bin/getAlignmentWindows -rwxr-xr-x root/root 140812 2018-12-04 09:03 ./usr/bin/getOrthologList -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/makeBadgerMatrix -rwxr-xr-x root/root 142340 2018-12-04 09:03 ./usr/bin/mauveAligner -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/mauveToXMFA -rwxr-xr-x root/root 13836 2018-12-04 09:03 ./usr/bin/mfa2xmfa -rwxr-xr-x root/root 203780 2018-12-04 09:03 ./usr/bin/progressiveMauve -rwxr-xr-x root/root 116236 2018-12-04 09:03 ./usr/bin/projectAndStrip -rwxr-xr-x root/root 124428 2018-12-04 09:03 ./usr/bin/randomGeneSample -rwxr-xr-x root/root 351276 2018-12-04 09:03 ./usr/bin/repeatoire -rwxr-xr-x root/root 95756 2018-12-04 09:03 ./usr/bin/scoreAlignment -rwxr-xr-x root/root 91660 2018-12-04 09:03 ./usr/bin/stripGapColumns -rwxr-xr-x root/root 95756 2018-12-04 09:03 ./usr/bin/stripSubsetLCBs -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/toGrimmFormat -rwxr-xr-x root/root 87564 2018-12-04 09:03 ./usr/bin/toMultiFastA -rwxr-xr-x root/root 9740 2018-12-04 09:03 ./usr/bin/toRawSequence -rwxr-xr-x root/root 9740 2018-12-04 09:03 ./usr/bin/uniqueMerCount -rwxr-xr-x root/root 42456 2018-12-04 09:03 ./usr/bin/uniquifyTrees -rwxr-xr-x root/root 91660 2018-12-04 09:03 ./usr/bin/xmfa2maf drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/ drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/doc/progressivemauve/ -rw-r--r-- root/root 261 2018-12-04 09:03 ./usr/share/doc/progressivemauve/README.test -rw-r--r-- root/root 818 2018-12-04 09:03 ./usr/share/doc/progressivemauve/changelog.Debian.gz -rw-r--r-- root/root 776 2018-12-04 09:03 ./usr/share/doc/progressivemauve/copyright -rw-r--r-- root/root 1244 2018-12-04 09:03 ./usr/share/doc/progressivemauve/run-unit-test drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/ -rw-r--r-- root/root 2203 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/all_virii.fasta.gz -rw-r--r-- root/root 2848 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_1.gbk.gz -rw-r--r-- root/root 2879 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_2.gbk.gz -rw-r--r-- root/root 2878 2018-12-04 09:03 ./usr/share/doc/progressivemauve/test_data/genome_3.gbk.gz drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/man/ drwxr-xr-x root/root 0 2018-12-04 09:03 ./usr/share/man/man1/ -rw-r--r-- root/root 1122 2018-12-04 09:03 ./usr/share/man/man1/addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/alignmentProjector.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/backbone_global_to_local.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/bbAnalyze.1.gz -> addUnalignedIntervals.1.gz -rw-r--r-- root/root 515 2018-12-04 09:03 ./usr/share/man/man1/bbFilter.1.gz -rw-r--r-- root/root 373 2018-12-04 09:03 ./usr/share/man/man1/coordinateTranslate.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/createBackboneMFA.1.gz -> addUnalignedIntervals.1.gz -rw-r--r-- root/root 525 2018-12-04 09:03 ./usr/share/man/man1/extractBCITrees.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/getAlignmentWindows.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/getOrthologList.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/makeBadgerMatrix.1.gz -> addUnalignedIntervals.1.gz -rw-r--r-- root/root 1516 2018-12-04 09:03 ./usr/share/man/man1/mauveAligner.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/mauveToXMFA.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/mfa2xmfa.1.gz -> addUnalignedIntervals.1.gz -rw-r--r-- root/root 1987 2018-12-04 09:03 ./usr/share/man/man1/progressiveMauve.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/projectAndStrip.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/randomGeneSample.1.gz -> addUnalignedIntervals.1.gz -rw-r--r-- root/root 919 2018-12-04 09:03 ./usr/share/man/man1/repeatoire.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/scoreAlignment.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/stripGapColumns.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/stripSubsetLCBs.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/toGrimmFormat.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/toMultiFastA.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/toRawSequence.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/uniqueMerCount.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/uniquifyTrees.1.gz -> addUnalignedIntervals.1.gz lrwxrwxrwx root/root 0 2018-12-04 09:03 ./usr/share/man/man1/xmfa2maf.1.gz -> addUnalignedIntervals.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 190416 Build-Time: 329 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 30 Job: progressivemauve_1.2.0+4713+dfsg-4 Lintian: pass Machine Architecture: amd64 Package: progressivemauve Package-Time: 370 Source-Version: 1.2.0+4713+dfsg-4 Space: 190416 Status: successful Version: 1.2.0+4713+dfsg-4 -------------------------------------------------------------------------------- Finished at 2019-05-30T13:18:21Z Build needed 00:06:10, 190416k disk space