sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | libmems 1.6.0+4725-8 (armhf) Sat, 01 Feb 2020 18:12:19 +0000 | +==============================================================================+ Package: libmems Version: 1.6.0+4725-8 Source Version: 1.6.0+4725-8 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-ac080f95-4fb4-4369-a9ec-d23ebe1bfb05' with '<>' I: NOTICE: Log filtering will replace 'build/libmems-D9UwW0/resolver-D0iViW' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-01-0814.04.pdiff [7567 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-01-1426.58.pdiff [8293 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-01-1426.58.pdiff [8293 B] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-01-0814.04.pdiff [17.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-01-1426.58.pdiff [11.6 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-01-1426.58.pdiff [11.6 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main armhf Packages [7960 kB] Fetched 8204 kB in 2s (4260 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libgmp10 libsystemd0 libudev1 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 763 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libsystemd0 amd64 244.1-2 [347 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libgmp10 amd64 2:6.2.0+dfsg-3 [253 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libudev1 amd64 244.1-2 [163 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 763 kB in 0s (13.7 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12778 files and directories currently installed.) Preparing to unpack .../libsystemd0_244.1-2_amd64.deb ... Unpacking libsystemd0:amd64 (244.1-2) over (244.1-1) ... Setting up libsystemd0:amd64 (244.1-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12778 files and directories currently installed.) Preparing to unpack .../libudev1_244.1-2_amd64.deb ... Unpacking libudev1:amd64 (244.1-2) over (244.1-1) ... Setting up libudev1:amd64 (244.1-2) ... Processing triggers for libc-bin (2.29-9) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'libmems' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libmems.git Please use: git clone https://salsa.debian.org/med-team/libmems.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 248 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main libmems 1.6.0+4725-8 (dsc) [2168 B] Get:2 http://debian.oregonstate.edu/debian unstable/main libmems 1.6.0+4725-8 (tar) [237 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main libmems 1.6.0+4725-8 (diff) [8696 B] Fetched 248 kB in 0s (5145 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/libmems-D9UwW0/libmems-1.6.0+4725' with '<>' I: NOTICE: Log filtering will replace 'build/libmems-D9UwW0' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [461 B] Get:5 copy:/<>/apt_archive ./ Packages [545 B] Fetched 1963 B in 0s (102 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils build-essential cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross 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-system1.67-dev:armhf libboost-system1.67.0:armhf libboost1.67-dev:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libgenome-dev:armhf libgenome0:armhf libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu-dev:armhf libicu63 libicu63:armhf libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmuscle-dev:armhf libmuscle1:armhf libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db pkg-config po-debconf sensible-utils ucf zlib1g:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff 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-contract1.67-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 glibc-doc manpages-dev:armhf icu-doc:armhf libstdc++-9-doc libstdc++-9-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils build-essential cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross 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-system1.67-dev:armhf libboost-system1.67.0:armhf libboost1.67-dev:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libgenome-dev:armhf libgenome0:armhf libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu-dev:armhf libicu63 libicu63:armhf libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmuscle-dev:armhf libmuscle1:armhf libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db pkg-config po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils ucf zlib1g:armhf 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 107 MB of archives. After this operation, 537 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [972 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.2.1-25 [195 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.33.90.20200122-2 [2748 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.10-10 [104 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-9 [2636 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-25 [1677 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-25 [10.7 MB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf-base amd64 9.2.1-21cross1 [194 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabihf amd64 9.2.1-21cross1 [6813 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [16.7 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-21cross1 [190 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.29-9cross1 [1110 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:9.2.1-21cross1 [37.3 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 9.2.1-21cross1 [73.2 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 9.2.1-21cross1 [6624 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 9.2.1-21cross1 [362 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 9.2.1-21cross1 [392 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 9.2.1-21cross1 [112 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armhf-cross all 9.2.1-21cross1 [664 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf amd64 9.2.1-21cross1 [7159 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1476 B] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 5.4.8-1cross1 [1128 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.29-9cross1 [2110 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armhf-cross all 9.2.1-21cross1 [1720 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabihf amd64 9.2.1-21cross1 [7390 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1184 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-8 [710 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.8 [6644 B] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 d-shlibs all 0.88 [17.4 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.4-1+b1 [1319 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 icu-devtools amd64 63.2-2 [189 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:9.2.1-25 [37.3 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt1 armhf 1:4.4.10-10 [101 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.29-9 [2328 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.2.1-25 [370 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 9.2.1-25 [6864 B] Get:87 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 9.2.1-25 [75.2 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 9.2.1-25 [432 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 9.2.1-25 [113 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-9-dev armhf 9.2.1-25 [663 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.4.13-1 [1040 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt-dev armhf 1:4.4.10-10 [120 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.29-9 [2129 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-9-dev armhf 9.2.1-25 [1721 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.67.0 armhf 1.67.0-17 [229 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.67.0 armhf 1.67.0-17 [255 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.67-dev armhf 1.67.0-17 [232 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.67-dev armhf 1.67.0-17 [264 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem-dev armhf 1.67.0.2+b1 [4304 B] Get:101 http://debian.oregonstate.edu/debian unstable/main armhf libicu63 armhf 63.2-2 [8005 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armhf libboost-regex1.67.0 armhf 1.67.0-17 [460 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armhf libicu-dev armhf 63.2-2 [8938 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armhf libboost-regex1.67-dev armhf 1.67.0-17 [562 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armhf libbz2-1.0 armhf 1.0.8-2 [44.4 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1+b1 [85.1 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams1.67.0 armhf 1.67.0-17 [246 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams1.67-dev armhf 1.67.0-17 [256 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armhf libboost-iostreams-dev armhf 1.67.0.2+b1 [4252 B] Get:110 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.67.0 armhf 1.67.0-17 [337 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.67-dev armhf 1.67.0-17 [387 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options-dev armhf 1.67.0.2+b1 [4280 B] Get:113 http://debian.oregonstate.edu/debian unstable/main armhf libgenome0 armhf 1.3.11+svn20110227.4616-2 [98.1 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armhf libgenome-dev armhf 1.3.11+svn20110227.4616-2 [174 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armhf libmuscle1 armhf 3.7+4565-6 [202 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armhf libmuscle-dev armhf 3.7+4565-6 [256 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main amd64 pkg-config amd64 0.29-6 [63.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 107 MB in 1s (71.4 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12778 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... 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Unpacking dwz (0.13-5) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../073-libglib2.0-0_2.62.4-1+b1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.62.4-1+b1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../074-libcroco3_0.6.13-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../075-gettext_0.19.8.1-10_amd64.deb ... Unpacking gettext (0.19.8.1-10) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../076-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../077-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../078-debhelper_12.9_all.deb ... Unpacking debhelper (12.9) ... 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Unpacking sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000002-1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.29-9cross1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.4-1+b1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.9) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:armhf (5.4.13-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libyaml-perl (1.30-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up gcc-9-arm-linux-gnueabihf-base:amd64 (9.2.1-21cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up linux-libc-dev-armhf-cross (5.4.8-1cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up icu-devtools (63.2-2) ... Setting up pkg-config (0.29-6) ... Setting up d-shlibs (0.88) ... Setting up gcc-9-cross-base (9.2.1-21cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.10-10) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.29-9) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up binutils-arm-linux-gnueabihf (2.33.90.20200122-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armhf (9.2.1-25) ... Setting up libgomp1-armhf-cross (9.2.1-21cross1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libstdc++-9-dev:amd64 (9.2.1-25) ... Setting up libtool (2.4.6-11) ... Setting up cpp-9-arm-linux-gnueabihf (9.2.1-21cross1) ... Setting up libc6-dev-armhf-cross (2.29-9cross1) ... Setting up m4 (1.4.18-4) ... Setting up libatomic1-armhf-cross (9.2.1-21cross1) ... Setting up libgcc1-armhf-cross (1:9.2.1-21cross1) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.2.1-25) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up build-essential (12.8) ... Setting up cpp-arm-linux-gnueabihf (4:9.2.1-3.1) ... 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 gettext (0.19.8.1-10) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+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 (9.2.1-21cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libstdc++6-armhf-cross (9.2.1-21cross1) ... Setting up libubsan1-armhf-cross (9.2.1-21cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-9-dev-armhf-cross (9.2.1-21cross1) ... Setting up po-debconf (1.0.21) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-9-arm-linux-gnueabihf (9.2.1-21cross1) ... Setting up libstdc++-9-dev-armhf-cross (9.2.1-21cross1) ... Setting up gcc-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-9-arm-linux-gnueabihf (9.2.1-21cross1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up g++-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.8) ... Setting up libcrypt1:armhf (1:4.4.10-10) ... Setting up dh-autoreconf (19) ... Setting up libc6:armhf (2.29-9) ... Setting up libcrypt-dev:armhf (1:4.4.10-10) ... Setting up libc6-dev:armhf (2.29-9) ... Setting up libbz2-1.0:armhf (1.0.8-2) ... Setting up libgcc1:armhf (1:9.2.1-25) ... Setting up debhelper (12.9) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1+b1) ... Setting up libgomp1:armhf (9.2.1-25) ... Setting up libasan5:armhf (9.2.1-25) ... Setting up libatomic1:armhf (9.2.1-25) ... Setting up libstdc++6:armhf (9.2.1-25) ... Setting up libboost-program-options1.67.0:armhf (1.67.0-17) ... 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 libicu63:armhf (63.2-2) ... Setting up libmuscle-dev:armhf (3.7+4565-6) ... Setting up libboost-iostreams1.67.0:armhf (1.67.0-17) ... Setting up libubsan1:armhf (9.2.1-25) ... Setting up libboost-system1.67.0:armhf (1.67.0-17) ... Setting up libicu-dev:armhf (63.2-2) ... Setting up libboost-regex1.67.0:armhf (1.67.0-17) ... Setting up libgcc-9-dev:armhf (9.2.1-25) ... Setting up libboost-filesystem1.67.0:armhf (1.67.0-17) ... Setting up libstdc++-9-dev:armhf (9.2.1-25) ... Setting up libboost1.67-dev:armhf (1.67.0-17) ... Setting up libboost-program-options1.67-dev:armhf (1.67.0-17) ... Setting up libboost-regex1.67-dev:armhf (1.67.0-17) ... Setting up libboost-program-options-dev:armhf (1.67.0.2+b1) ... Setting up libboost-system1.67-dev:armhf (1.67.0-17) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-17) ... Setting up libboost-filesystem1.67-dev:armhf (1.67.0-17) ... Setting up libboost-iostreams-dev:armhf (1.67.0.2+b1) ... Setting up libboost-filesystem-dev:armhf (1.67.0.2+b1) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.29-9) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.33.90.20200122-2 dpkg-dev_1.19.7 g++-9_9.2.1-25 gcc-8_8.3.0-26 gcc-9_9.2.1-25 libc6-dev_2.29-9 libstdc++-9-dev_9.2.1-25 libstdc++-9-dev-armhf-cross_9.2.1-21cross1 libstdc++6_9.2.1-25 libstdc++6-armhf-cross_9.2.1-21cross1 linux-libc-dev_5.4.13-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2 binutils-arm-linux-gnueabihf_2.33.90.20200122-2 binutils-common_2.33.90.20200122-2 binutils-x86-64-linux-gnu_2.33.90.20200122-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-26 cpp-9_9.2.1-25 cpp-9-arm-linux-gnueabihf_9.2.1-21cross1 cpp-arm-linux-gnueabihf_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.8 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-25 g++-9-arm-linux-gnueabihf_9.2.1-21cross1 g++-arm-linux-gnueabihf_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-26 gcc-8-base_8.3.0-26 gcc-9_9.2.1-25 gcc-9-arm-linux-gnueabihf_9.2.1-21cross1 gcc-9-arm-linux-gnueabihf-base_9.2.1-21cross1 gcc-9-base_9.2.1-25 gcc-9-cross-base_9.2.1-21cross1 gcc-arm-linux-gnueabihf_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25 libasan5-armhf-cross_9.2.1-21cross1 libatomic1_9.2.1-25 libatomic1-armhf-cross_9.2.1-21cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2 libblkid1_2.34-0.1 libboost-filesystem-dev_1.67.0.2+b1 libboost-filesystem1.67-dev_1.67.0-17 libboost-filesystem1.67.0_1.67.0-17 libboost-iostreams-dev_1.67.0.2+b1 libboost-iostreams1.67-dev_1.67.0-17 libboost-iostreams1.67.0_1.67.0-17 libboost-program-options-dev_1.67.0.2+b1 libboost-program-options1.67-dev_1.67.0-17 libboost-program-options1.67.0_1.67.0-17 libboost-regex1.67-dev_1.67.0-17 libboost-regex1.67.0_1.67.0-17 libboost-system1.67-dev_1.67.0-17 libboost-system1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-9 libc-dev-bin_2.29-9 libc6_2.29-9 libc6-armhf-cross_2.29-9cross1 libc6-dev_2.29-9 libc6-dev-armhf-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_9.2.1-25 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.33.90.20200122-2 libctf0_2.33.90.20200122-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-3 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-26 libgcc-9-dev_9.2.1-25 libgcc-9-dev-armhf-cross_9.2.1-21cross1 libgcc1_1:9.2.1-25 libgcc1-armhf-cross_1:9.2.1-21cross1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgenome-dev_1.3.11+svn20110227.4616-2 libgenome0_1.3.11+svn20110227.4616-2 libglib2.0-0_2.62.4-1+b1 libgmp10_2:6.2.0+dfsg-3 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25 libgomp1-armhf-cross_9.2.1-21cross1 libgpg-error0_1.36-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22-2 libitm1_9.2.1-25 liblocale-gettext-perl_1.07-4 liblsan0_9.2.1-25 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-26 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libquadmath0_9.2.1-25 libseccomp2_2.4.2-2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.5-2 libstdc++-9-dev_9.2.1-25 libstdc++-9-dev-armhf-cross_9.2.1-21cross1 libstdc++6_9.2.1-25 libstdc++6-armhf-cross_9.2.1-21cross1 libsub-override-perl_0.09-2 libsystemd0_244.1-2 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libtsan0_9.2.1-25 libubsan1_9.2.1-25 libubsan1-armhf-cross_9.2.1-21cross1 libuchardet0_0.0.6-3 libudev1_244.1-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-8 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.4.13-1 linux-libc-dev-armhf-cross_5.4.8-1cross1 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 pkg-config_0.29-6 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libmems Binary: libmems-dev, libmems1 Architecture: any Version: 1.6.0+4725-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/libmems Vcs-Git: https://salsa.debian.org/med-team/libmems.git Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev Package-List: libmems-dev deb libdevel optional arch=any libmems1 deb libs optional arch=any Checksums-Sha1: 717cab0cd606be4ebdb1b5990ee89a85d8d6c39b 236796 libmems_1.6.0+4725.orig.tar.xz 61694e63abfd068b08762e5ab5f5ead4fb8e96bd 8696 libmems_1.6.0+4725-8.debian.tar.xz Checksums-Sha256: 67265e1eb1b85a04533be431b906cc8d4773c799fb1a7809b346209380c41e91 236796 libmems_1.6.0+4725.orig.tar.xz a5877395d9cd6ec389895cbf39b5aa3c8a688b943b1f62aabf04ef9c576dab21 8696 libmems_1.6.0+4725-8.debian.tar.xz Files: a3f12384cfcf888f01b39f562024d5e8 236796 libmems_1.6.0+4725.orig.tar.xz 055e67cca13777db163288075def9d1e 8696 libmems_1.6.0+4725-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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19:51:46 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 ./libmems_1.6.0+4725-8.dsc dpkg-source: info: extracting libmems in /<> dpkg-source: info: unpacking libmems_1.6.0+4725.orig.tar.xz dpkg-source: info: unpacking libmems_1.6.0+4725-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_fix_ctors.patch dpkg-source: info: applying 02_fix_a_Wformat.patch dpkg-source: info: applying pkg-config-directive.patch dpkg-source: info: applying 03_update_boost_m4_to_git_d9ff75.patch dpkg-source: info: applying 04_add_dependend_libs_to_link_command.patch dpkg-source: info: applying 05_gcc-6.patch dpkg-source: info: applying boost1.62.patch dpkg-source: info: applying drop-version-number.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=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-ac080f95-4fb4-4369-a9ec-d23ebe1bfb05 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package libmems dpkg-buildpackage: info: source version 1.6.0+4725-8 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 libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:54: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.ac:66: installing 'config/compile' configure.ac:66: installing 'config/config.guess' configure.ac:66: installing 'config/config.sub' configure.ac:54: installing 'config/install-sh' configure.ac:54: installing 'config/missing' libMems/Makefile.am:48: warning: source file 'HomologyHMM/algebras.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. libMems/Makefile.am:48: warning: source file 'HomologyHMM/homology.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:48: warning: source file 'HomologyHMM/homologymain.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/asyncio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alinuxaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/aPOSIXaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alibc.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/awin32aio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/buffer.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/util.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sorting.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/dmsort.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/timing.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sml.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am: installing 'config/depcomp' 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 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-g++... arm-linux-gnueabihf-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether arm-linux-gnueabihf-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabihf-g++... none checking whether ln -s works... yes checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking for arm-linux-gnueabihf-gcc... arm-linux-gnueabihf-gcc 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 dependency style of arm-linux-gnueabihf-gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by arm-linux-gnueabihf-gcc... /usr/arm-linux-gnueabihf/bin/ld checking if the linker (/usr/arm-linux-gnueabihf/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/arm-linux-gnueabihf-nm -B checking the name lister (/usr/bin/arm-linux-gnueabihf-nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/arm-linux-gnueabihf/bin/ld option to reload object files... -r checking for arm-linux-gnueabihf-objdump... arm-linux-gnueabihf-objdump checking how to recognize dependent libraries... pass_all checking for arm-linux-gnueabihf-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for arm-linux-gnueabihf-ar... arm-linux-gnueabihf-ar checking for archiver @FILE support... @ checking for arm-linux-gnueabihf-strip... (cached) arm-linux-gnueabihf-strip checking for arm-linux-gnueabihf-ranlib... arm-linux-gnueabihf-ranlib checking command to parse /usr/bin/arm-linux-gnueabihf-nm -B output from arm-linux-gnueabihf-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for arm-linux-gnueabihf-mt... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E checking for ANSI C header files... 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 for dlfcn.h... yes checking for objdir... .libs checking if arm-linux-gnueabihf-gcc supports -fno-rtti -fno-exceptions... no checking for arm-linux-gnueabihf-gcc option to produce PIC... -fPIC -DPIC checking if arm-linux-gnueabihf-gcc PIC flag -fPIC -DPIC works... yes checking if arm-linux-gnueabihf-gcc static flag -static works... yes checking if arm-linux-gnueabihf-gcc supports -c -o file.o... yes checking if arm-linux-gnueabihf-gcc supports -c -o file.o... (cached) yes checking whether the arm-linux-gnueabihf-gcc linker (/usr/arm-linux-gnueabihf/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... arm-linux-gnueabihf-g++ -E checking for ld used by arm-linux-gnueabihf-g++... /usr/arm-linux-gnueabihf/bin/ld checking if the linker (/usr/arm-linux-gnueabihf/bin/ld) is GNU ld... yes checking whether the arm-linux-gnueabihf-g++ linker (/usr/arm-linux-gnueabihf/bin/ld) supports shared libraries... yes checking for arm-linux-gnueabihf-g++ option to produce PIC... -fPIC -DPIC checking if arm-linux-gnueabihf-g++ PIC flag -fPIC -DPIC works... yes checking if arm-linux-gnueabihf-g++ static flag -static works... yes checking if arm-linux-gnueabihf-g++ supports -c -o file.o... yes checking if arm-linux-gnueabihf-g++ supports -c -o file.o... (cached) yes checking whether the arm-linux-gnueabihf-g++ linker (/usr/arm-linux-gnueabihf/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for ANSI C header files... (cached) yes checking for Boost headers version >= 1.34.0... yes checking for Boost's header version... 1_67 checking whether the compiler implements namespaces... yes checking for the toolset name used by Boost for arm-linux-gnueabihf-g++... configure: WARNING: could not figure out which toolset name to use for arm-linux-gnueabihf-g++ checking boost/system/error_code.hpp usability... yes checking boost/system/error_code.hpp presence... yes checking for boost/system/error_code.hpp... yes checking for the Boost system library... yes checking boost/filesystem/path.hpp usability... yes checking boost/filesystem/path.hpp presence... yes checking for boost/filesystem/path.hpp... yes checking for the Boost filesystem library... (cached) yes checking boost/program_options.hpp usability... yes checking boost/program_options.hpp presence... yes checking for boost/program_options.hpp... yes checking for the Boost program_options library... (cached) yes checking boost/iostreams/device/file_descriptor.hpp usability... yes checking boost/iostreams/device/file_descriptor.hpp presence... yes checking for boost/iostreams/device/file_descriptor.hpp... yes checking for the Boost iostreams library... (cached) 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 sys/types.h... (cached) yes checking sys/aio.h usability... no checking sys/aio.h presence... no checking for sys/aio.h... no checking aio.h usability... yes checking aio.h presence... yes checking for aio.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking for pthread_mutex_unlock in -lpthread... yes checking for aio_write in -lrt... yes checking for arm-linux-gnueabihf-doxygen... no checking for doxygen... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for arm-linux-gnueabihf-perl... no checking for perl... /usr/bin/perl configure: WARNING: using cross tools not prefixed with host triplet 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 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 libMems/Makefile config.status: creating libMems.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in libMems make[3]: Entering directory '/<>/libMems' /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ MatchFinder.cpp:126:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 126 | } | ^ MatchFinder.cpp:126:1: 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++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual boolean mems::MemorySML::Read(std::vector&, gnSeqI, gnSeqI)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from MemorySML.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from MemorySML.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from MemorySML.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In member function ‘virtual void mems::MemorySML::Create(const genome::gnSequence&, uint64)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::SortedMerList::FindAll(const string&, std::vector)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ SortedMerList.cpp:229:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 229 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::SortedMerList::FillSML(gnSeqI, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ SortedMerList.cpp:579:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 579 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::SortedMerList::FillDnaSML(const genome::gnSequence&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::FileSML::RadixSort(std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::FileSML::LoadFile(const string&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/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::bmer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::FileSML::Merge(mems::SortedMerList&, mems::SortedMerList&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/dispatch.hpp:17, from /usr/include/boost/iostreams/flush.hpp:17, from /usr/include/boost/iostreams/close.hpp:18, from /usr/include/boost/iostreams/device/mapped_file.hpp:20, from ../libMems/FileSML.h:22, from FileSML.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In member function ‘virtual void mems::FileSML::Create(const genome::gnSequence&, uint64)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘virtual void mems::MemHash::FindMatches(mems::MatchList&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/UngappedLocalAlignment.h:18, from ../libMems/Match.h:19, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/UngappedLocalAlignment.h:18, from ../libMems/Match.h:19, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/MatchHashEntry.h:19, from MatchHashEntry.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 202 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Aligner.cpp:10: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::CreateGapSearchList(std::vector&, const std::vector&, std::vector > >&, boolean)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/GappedAligner.h:18, from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 202 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: 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++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: 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++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: 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++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/GappedAligner.h:17, from ../libMems/Aligner.h:18, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::computeLCBAdjacencies_v2(mems::IntervalList&, std::vector >&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::computeLCBAdjacencies_v2(std::vector >*> >&, std::vector >&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >*> >&, boolean, std::ostream*)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::string)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::Island&}; _Tp = mems::Island; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::simpleFindIslands(mems::IntervalList&, uint, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/Interval.h:21, from ../libMems/IntervalList.h:22, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/Interval.h:18, from ../libMems/IntervalList.h:22, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GappedAlignment&}; _Tp = mems::GappedAlignment; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::simpleFindBackbone(mems::IntervalList&, uint, uint, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In function ‘void mems::addUnalignedIntervals(mems::IntervalList&, std::set, std::vector)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/MatchFinder.h:17, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/GappedAlignment.h:18, from GappedAlignment.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/GappedAlignment.h:18, from GappedAlignment.cpp:13: ../libMems/SparseAbstractMatch.h:144:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 144 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: ../libMems/SparseAbstractMatch.h:144:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 144 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ MuscleInterface.cpp:519:1: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 519 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/Matrix.h:19, from ../libMems/NumericMatrix.h:16, from ../libMems/MuscleInterface.h:16, from MuscleInterface.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ MuscleInterface.cpp:672:1: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 672 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, from ../libMems/SortedMerList.h:19, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/RepeatMatchList.h:20, from RepeatMatchList.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/MatchHashEntry.h:19, from ../libMems/RepeatMatch.h:20, from RepeatMatch.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 202 | } | ^ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::MatchProjectionAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/Interval.h:21, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector*>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::getBpList(MatchVector&, uint, std::vector&) [with MatchVector = std::vector >*, std::allocator >*> >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::unalignIslands(mems::IntervalList&, std::vector*>&, std::vector >*, std::allocator >*> > >&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::SuperInterval&}; _Tp = mems::SuperInterval; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::applyBreakpoints(std::vector&, std::vector&, Maniplator&) [with T = mems::SuperInterval; Maniplator = mems::SuperIntervalManipulator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from ../libMems/Match.h:22, from ../libMems/Interval.h:21, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: ../libMems/HybridAbstractMatch.h:202:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 202 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_equal_to_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:962:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 962 | __unique(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:962:5: 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++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:184:5: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::chooseNextAlignmentPair(PhyloTree&, node_id_t&, node_id_t&, node_id_t&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mems::GenericInterval, std::allocator > > >}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘double mems::greedySearch(SearchScorer&) [with SearchScorer = mems::EvenFasterSumOfPairsBreakpointScorer]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 397 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:721:7: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::GreedyRemovalScorer]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 397 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:397:23: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 1662 | _M_range_insert(__pos, __first, __last, | ^~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1662:4: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 397 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:397:23: 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++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::AlignmentTreeNode&}; _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘node_id_t mems::createAlignmentTreeRoot(PhyloTree&, node_id_t, node_id_t)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = mems::AlignmentTreeNode]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericIntervalList<>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::makeAlignmentTree(PhyloTree&, MatchListType&, std::vector&) [with MatchListType = mems::GenericMatchList >*>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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 int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::applyAncestralBreakpoints(const std::vector&, std::vector&, uint, Manipulator&) [with T = mems::AbstractMatch*; Manipulator = mems::GenericMatchSeqManipulator<>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::applyAncestralBreakpoints(const std::vector&, std::vector&, uint, Manipulator&) [with T = mems::SuperInterval; Manipulator = mems::SuperIntervalManipulator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(node_id_t)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1004:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1004 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1005 | __gnu_cxx::__ops::__iter_equal_to_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = std::vector]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = mems::GenericMatchList >*>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1004:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1004 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1005 | __gnu_cxx::__ops::__iter_equal_to_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = mems::GenericMatchList >*>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::ProgressiveAligner::pairwiseAnchorSearch(mems::MatchList&, mems::Match*, mems::Match*, const mems::AbstractMatch*, uint, uint)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void mems::ProgressiveAligner::recurseOnPairs(const std::vector&, const std::vector&, const GappedAlignmentType&, Matrix >*> >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, boost::multi_array >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 923 | } | ^ ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 ProgressiveAligner.cpp:923:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 ProgressiveAligner.cpp:923:1: 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++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In member function ‘void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void mems::ProgressiveAligner::getAlignment(mems::IntervalList&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 171 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: ../libMems/SparseAbstractMatch.h:195:1: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 195 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1428 | { return _M_erase(begin() + (__position - cbegin())); } | ^ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/Interval.h:18, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from GreedyBreakpointElimination.cpp:7: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: 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++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from ../libMems/AbstractMatch.h:18, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from ../libMems/AbstractMatch.h:17, from ../libMems/GreedyBreakpointElimination.h:8, from GreedyBreakpointElimination.cpp:6: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In constructor ‘mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array, boost::multi_array, std::vector*>, mems::PairwiseLCBMatrix&, std::vector&, std::vector&, boost::multi_array&, boost::multi_array&, size_t, size_t, size_t, size_t)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/arm-linux-gnueabihf/include/c++/9/backward/hashtable.h:62, from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/arm-linux-gnueabihf/include/c++/9/backward/hashtable.h:62, from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:64, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘void SimplePath::addEdge(int, double, std::vector&, int, int)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o In file included from /usr/arm-linux-gnueabihf/include/c++/9/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homologymain.cc:21: /usr/arm-linux-gnueabihf/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ libtool: compile: arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o dmSML/aPOSIXaio.c: In function ‘QueryLastCompletePAIO’: dmSML/aPOSIXaio.c:115:21: warning: passing argument 1 of ‘aio_suspend’ from incompatible pointer type [-Wincompatible-pointer-types] 115 | rval = aio_suspend(request_array, 1, &zero_wait); | ^~~~~~~~~~~~~ | | | struct aiocb ** In file included from /usr/arm-linux-gnueabihf/include/features.h:446, from /usr/arm-linux-gnueabihf/include/sys/types.h:25, from ../libMems/dmSML/asyncio.h:24, from ../libMems/dmSML/aPOSIXaio.h:8, from dmSML/aPOSIXaio.c:5: /usr/arm-linux-gnueabihf/include/aio.h:198:12: note: expected ‘const struct aiocb * const*’ but argument is of type ‘struct aiocb **’ 198 | extern int __REDIRECT_NTH (aio_suspend, | ^~~~~~~~~~~~~~ libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o dmSML/util.c: In function ‘removeFile’: dmSML/util.c:126:24: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 126 | rm_cmd = Fmt( "/bin/rm -fv %s", filename ); | ^ dmSML/util.c:128:24: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 128 | rm_cmd = Fmt( "/bin/rm -f %s", filename ); | ^ dmSML/util.c:129:16: warning: implicit declaration of function ‘system’ [-Wimplicit-function-declaration] 129 | return system( rm_cmd ); | ^~~~~~ libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o libtool: compile: arm-linux-gnueabihf-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link arm-linux-gnueabihf-g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/arm-linux-gnueabihf RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -L/usr/lib/arm-linux-gnueabihf -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread libtool: link: arm-linux-gnueabihf-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc-cross/arm-linux-gnueabihf/9/../../../../arm-linux-gnueabihf/lib/crti.o /usr/lib/gcc-cross/arm-linux-gnueabihf/9/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -L/usr/lib/arm-linux-gnueabihf -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc-cross/arm-linux-gnueabihf/9 -L/usr/lib/gcc-cross/arm-linux-gnueabihf/9/../../../../arm-linux-gnueabihf/lib -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc-cross/arm-linux-gnueabihf/9/crtendS.o /usr/lib/gcc-cross/arm-linux-gnueabihf/9/../../../../arm-linux-gnueabihf/lib/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems.so.1 -o .libs/libMems.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libMems.so.1" && ln -s "libMems.so.1.0.0" "libMems.so.1") libtool: link: (cd ".libs" && rm -f "libMems.so" && ln -s "libMems.so.1.0.0" "libMems.so") libtool: link: arm-linux-gnueabihf-ar cru .libs/libMems.a RepeatHash.o DNAFileSML.o MatchFinder.o DNAMemorySML.o MemorySML.o SortedMerList.o FileSML.o MemHash.o MatchHashEntry.o Interval.o IntervalList.o twister.o gnAlignedSequences.o MatchList.o Aligner.o Islands.o MaskedMemHash.o GappedAlignment.o MuscleInterface.o PhyloTree.o RepeatMatchList.o RepeatMatch.o Backbone.o PairwiseMatchFinder.o ProgressiveAligner.o SuperInterval.o GreedyBreakpointElimination.o algebras.o homology.o homologymain.o asyncio.o alinuxaio.o aPOSIXaio.o alibc.o awin32aio.o buffer.o util.o sorting.o dmsort.o timing.o sml.o arm-linux-gnueabihf-ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: arm-linux-gnueabihf-ranlib .libs/libMems.a libtool: link: ( cd ".libs" && rm -f "libMems.la" && ln -s "../libMems.la" "libMems.la" ) make[3]: Leaving directory '/<>/libMems' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' 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=/<>/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in libMems make[2]: Entering directory '/<>/libMems' make[3]: Entering directory '/<>/libMems' /bin/mkdir -p '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ../libtool --mode=install /usr/bin/install -c libMems.la '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libMems.so.1.0.0 libMems.so.1 || { rm -f libMems.so.1 && ln -s libMems.so.1.0.0 libMems.so.1; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; }) libtool: install: /usr/bin/install -c .libs/libMems.lai /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.la libtool: install: /usr/bin/install -c .libs/libMems.a /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: install: arm-linux-gnueabihf-ranlib /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/<>/debian/tmp/usr/include/libMems/dmSML' /usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/<>/debian/tmp/usr/include/libMems/dmSML' /bin/mkdir -p '/<>/debian/tmp/usr/include/libMems/HomologyHMM' /usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/<>/debian/tmp/usr/include/libMems/HomologyHMM' /bin/mkdir -p '/<>/debian/tmp/usr/include/libMems' /usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/<>/debian/tmp/usr/include/libMems' /usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/<>/debian/tmp/usr/include/libMems' make[3]: Leaving directory '/<>/libMems' make[2]: Leaving directory '/<>/libMems' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 libMems.pc '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libGenome0-dev/libgenome-dev/ \ --override s/libMUSCLE1-dev/libmuscle-dev/ \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libboost-filesystem1.67-dev package exists. --> libboost-iostreams1.67-dev package exists. --> libgenome-dev package exists. --> libmuscle-dev package exists. set -e install -d -m 755 debian/libmems-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libmems1/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.a debian/libmems-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so debian/libmems-dev/usr/lib/arm-linux-gnueabihf mv /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1 debian/libmems1/usr/lib/arm-linux-gnueabihf mv /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 debian/libmems1/usr/lib/arm-linux-gnueabihf PKGDEV=libmems-dev PKGSHL=libmems1 install -d -m 755 debian/libmems-dev/usr mv debian/tmp/usr/include debian/libmems-dev/usr install -d -m 755 debian/libmems-dev/usr/lib/arm-linux-gnueabihf/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-dev/usr/lib/arm-linux-gnueabihf/pkgconfig make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -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: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libmems1/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 found in none of the libraries dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libmems-dev' in '../libmems-dev_1.6.0+4725-8_armhf.deb'. dpkg-deb: building package 'libmems1' in '../libmems1_1.6.0+4725-8_armhf.deb'. dpkg-deb: building package 'libmems1-dbgsym' in '../libmems1-dbgsym_1.6.0+4725-8_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../libmems_1.6.0+4725-8_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 2020-02-01T18:22:19Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libmems_1.6.0+4725-8_armhf.changes: ----------------------------------- Format: 1.8 Date: Mon, 27 Aug 2018 21:38:53 +0200 Source: libmems Binary: libmems-dev libmems1 libmems1-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.6.0+4725-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libmems-dev - development library to support DNA string matching and comparativ libmems1 - library to support DNA string matching and comparative genomics Closes: 907417 Changes: libmems (1.6.0+4725-8) unstable; urgency=medium . * Do not provide packages with different files Closes: #907417 * Standards-Version: 4.2.1 Checksums-Sha1: 439a72b7bc1a8582ee1711cf0b33636bd9473b6d 853104 libmems-dev_1.6.0+4725-8_armhf.deb 4cc6df018ea1e05caae1378a0e83014a0f698b1b 10924332 libmems1-dbgsym_1.6.0+4725-8_armhf.deb ff23cd78d1c9d47ba55adb14dbe99d97aa2c5bca 556004 libmems1_1.6.0+4725-8_armhf.deb 4fe120a3a108fb2fbe83c20c2f3724aa31f58a9e 6368 libmems_1.6.0+4725-8_armhf.buildinfo Checksums-Sha256: 7738b872545a4dd4169bb65535595391afc59bef605491ce91e7a5bc7dca794d 853104 libmems-dev_1.6.0+4725-8_armhf.deb 0e7bc0fc1621b0500761aaa9da33dfe9784d5c14a61d8eb1715df967cf422670 10924332 libmems1-dbgsym_1.6.0+4725-8_armhf.deb 0a88d08a76e8ac28bd1a97123e241534d3204564dde7e28b08230ff798523118 556004 libmems1_1.6.0+4725-8_armhf.deb 534b24724e3c2e353a502d3f4cc04ffdb9d53013cd7dcb3ea571cfadb5e20013 6368 libmems_1.6.0+4725-8_armhf.buildinfo Files: 116b99a9796c9542c3033e36e417a459 853104 libdevel optional libmems-dev_1.6.0+4725-8_armhf.deb 5cc300ac88ee1a9278d15edb1bd04c70 10924332 debug optional libmems1-dbgsym_1.6.0+4725-8_armhf.deb 822f1e23fe3893136d5ea429f1701bb1 556004 libs optional libmems1_1.6.0+4725-8_armhf.deb 7927772a3b331baede1026f783fa227a 6368 science optional libmems_1.6.0+4725-8_armhf.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: libmems Binary: libmems-dev libmems1 Architecture: armhf Version: 1.6.0+4725-8 Checksums-Md5: 116b99a9796c9542c3033e36e417a459 853104 libmems-dev_1.6.0+4725-8_armhf.deb 5cc300ac88ee1a9278d15edb1bd04c70 10924332 libmems1-dbgsym_1.6.0+4725-8_armhf.deb 822f1e23fe3893136d5ea429f1701bb1 556004 libmems1_1.6.0+4725-8_armhf.deb Checksums-Sha1: 439a72b7bc1a8582ee1711cf0b33636bd9473b6d 853104 libmems-dev_1.6.0+4725-8_armhf.deb 4cc6df018ea1e05caae1378a0e83014a0f698b1b 10924332 libmems1-dbgsym_1.6.0+4725-8_armhf.deb ff23cd78d1c9d47ba55adb14dbe99d97aa2c5bca 556004 libmems1_1.6.0+4725-8_armhf.deb Checksums-Sha256: 7738b872545a4dd4169bb65535595391afc59bef605491ce91e7a5bc7dca794d 853104 libmems-dev_1.6.0+4725-8_armhf.deb 0e7bc0fc1621b0500761aaa9da33dfe9784d5c14a61d8eb1715df967cf422670 10924332 libmems1-dbgsym_1.6.0+4725-8_armhf.deb 0a88d08a76e8ac28bd1a97123e241534d3204564dde7e28b08230ff798523118 556004 libmems1_1.6.0+4725-8_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 01 Feb 2020 18:22:19 +0000 Build-Path: /<> Installed-Build-Depends: adduser (= 3.118), apt (= 1.8.4), autoconf (= 2.69-11.1), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-5), binutils (= 2.33.90.20200122-2), binutils-common (= 2.33.90.20200122-2), binutils-x86-64-linux-gnu (= 2.33.90.20200122-2), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-26), cpp-9 (= 9.2.1-25), d-shlibs (= 0.88), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.9), debian-archive-keyring (= 2019.1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-5), fdisk (= 2.34-0.1), file (= 1:5.38-4), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-25), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-26), gcc-8-base (= 8.3.0-26), gcc-9 (= 9.2.1-25), gcc-9-base (= 9.2.1-25), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), gpgv (= 2.2.19-1), grep (= 3.4-1), groff-base (= 1.22.4-4), gzip (= 1.9-3+b1), hostname (= 3.23), icu-devtools (= 63.2-2), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libapt-pkg5.0 (= 1.8.4), libarchive-zip-perl (= 1.67-1), libasan5 (= 9.2.1-25), libatomic1 (= 9.2.1-25), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2+b1), libbinutils (= 2.33.90.20200122-2), libblkid1 (= 2.34-0.1), libboost-filesystem-dev (= 1.67.0.2+b1), libboost-filesystem1.67-dev (= 1.67.0-17), libboost-filesystem1.67.0 (= 1.67.0-17), libboost-iostreams-dev (= 1.67.0.2+b1), libboost-iostreams1.67-dev (= 1.67.0-17), libboost-iostreams1.67.0 (= 1.67.0-17), libboost-program-options-dev (= 1.67.0.2+b1), libboost-program-options1.67-dev (= 1.67.0-17), libboost-program-options1.67.0 (= 1.67.0-17), libboost-regex1.67-dev (= 1.67.0-17), libboost-regex1.67.0 (= 1.67.0-17), libboost-system1.67-dev (= 1.67.0-17), libboost-system1.67.0 (= 1.67.0-17), libboost1.67-dev (= 1.67.0-17), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-9), libc-dev-bin (= 2.29-9), libc6 (= 2.29-9), libc6-dev (= 2.29-9), libcap-ng0 (= 0.7.9-2.1+b1), libcc1-0 (= 9.2.1-25), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10), libcrypt1 (= 1:4.4.10-10), libctf-nobfd0 (= 2.33.90.20200122-2), libctf0 (= 2.33.90.20200122-2), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.251), libdebhelper-perl (= 12.9), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi7 (= 3.3-3), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-8-dev (= 8.3.0-26), libgcc-9-dev (= 9.2.1-25), libgcc1 (= 1:9.2.1-25), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libgenome-dev (= 1.3.11+svn20110227.4616-2), libgenome0 (= 1.3.11+svn20110227.4616-2), libglib2.0-0 (= 2.62.4-1+b1), libgmp10 (= 2:6.2.0+dfsg-3), libgnutls30 (= 3.6.11.1-2), libgomp1 (= 9.2.1-25), libgpg-error0 (= 1.36-7), libhogweed5 (= 3.5.1+really3.5.1-2), libicu-dev (= 63.2-2), libicu63 (= 63.2-2), libidn2-0 (= 2.2.0-2), libisl22 (= 0.22-2), libitm1 (= 9.2.1-25), liblsan0 (= 9.2.1-25), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-26), libmuscle-dev (= 3.7+4565-6), libmuscle1 (= 3.7+4565-6), libncursesw6 (= 6.1+20191019-1), libnettle7 (= 3.5.1+really3.5.1-2), libp11-kit0 (= 0.23.20-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-9), libpipeline1 (= 1.5.2-2), libquadmath0 (= 9.2.1-25), libseccomp2 (= 2.4.2-2), libselinux1 (= 3.0-1), libsemanage-common (= 3.0-1), libsemanage1 (= 3.0-1), libsepol1 (= 3.0-1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-25), libstdc++6 (= 9.2.1-25), libsub-override-perl (= 0.09-2), libsystemd0 (= 244.1-2), libtasn1-6 (= 4.15.0-2), libtinfo6 (= 6.1+20191019-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-25), libubsan1 (= 9.2.1-25), libuchardet0 (= 0.0.6-3), libudev1 (= 244.1-2), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-8), libzstd1 (= 1.4.4+dfsg-1), linux-libc-dev (= 5.4.13-1), login (= 1:4.8-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.0-2), mawk (= 1.3.4.20200120-1), ncurses-base (= 6.1+20191019-1), ncurses-bin (= 6.1+20191019-1), passwd (= 1:4.8-1), patch (= 2.7.6-6), perl (= 5.30.0-9), perl-base (= 5.30.0-9), perl-modules-5.30 (= 5.30.0-9), pkg-config (= 0.29-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1535398733" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libmems-dev_1.6.0+4725-8_armhf.deb ---------------------------------- new Debian package, version 2.0. size 853104 bytes: control archive=2908 bytes. 1184 bytes, 23 lines control 5014 bytes, 71 lines md5sums Package: libmems-dev Source: libmems Version: 1.6.0+4725-8 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 4688 Depends: libmems1 (= 1.6.0+4725-8), libboost-filesystem1.67-dev, libboost-iostreams1.67-dev, libgenome-dev, libmuscle-dev Provides: libmems-1.6-dev Section: libdevel Priority: optional Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Description: development library to support DNA string matching and comparative genomics libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements. . This is the development package containing the statically linked library and the header files. drwxr-xr-x root/root 0 2018-08-27 19:38 ./ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/include/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/include/libMems/ -rw-r--r-- root/root 3614 2018-08-27 19:38 ./usr/include/libMems/AbstractGappedAlignment.h -rw-r--r-- root/root 13029 2018-08-27 19:38 ./usr/include/libMems/AbstractMatch.h -rw-r--r-- root/root 11670 2018-08-27 19:38 ./usr/include/libMems/Aligner.h -rw-r--r-- root/root 8161 2018-08-27 19:38 ./usr/include/libMems/Backbone.h -rw-r--r-- root/root 26662 2018-08-27 19:38 ./usr/include/libMems/CompactGappedAlignment.h -rw-r--r-- root/root 2075 2018-08-27 19:38 ./usr/include/libMems/DNAFileSML.h -rw-r--r-- root/root 1905 2018-08-27 19:38 ./usr/include/libMems/DNAMemorySML.h -rw-r--r-- root/root 5031 2018-08-27 19:38 ./usr/include/libMems/DenseAbstractMatch.h -rw-r--r-- root/root 10891 2018-08-27 19:38 ./usr/include/libMems/DistanceMatrix.h -rw-r--r-- root/root 4590 2018-08-27 19:38 ./usr/include/libMems/FileSML.h -rw-r--r-- root/root 5777 2018-08-27 19:38 ./usr/include/libMems/Files.h -rw-r--r-- root/root 2513 2018-08-27 19:38 ./usr/include/libMems/GappedAligner.h -rw-r--r-- root/root 8478 2018-08-27 19:38 ./usr/include/libMems/GappedAlignment.h -rw-r--r-- root/root 29239 2018-08-27 19:38 ./usr/include/libMems/GreedyBreakpointElimination.h drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/include/libMems/HomologyHMM/ -rw-r--r-- root/root 20861 2018-08-27 19:38 ./usr/include/libMems/HomologyHMM/algebras.h -rw-r--r-- root/root 13161 2018-08-27 19:38 ./usr/include/libMems/HomologyHMM/dptables.h -rw-r--r-- root/root 7163 2018-08-27 19:38 ./usr/include/libMems/HomologyHMM/homology.h -rw-r--r-- root/root 7759 2018-08-27 19:38 ./usr/include/libMems/HomologyHMM/parameters.h -rw-r--r-- root/root 9786 2018-08-27 19:38 ./usr/include/libMems/HybridAbstractMatch.h -rw-r--r-- root/root 30049 2018-08-27 19:38 ./usr/include/libMems/Interval.h -rw-r--r-- root/root 27519 2018-08-27 19:38 ./usr/include/libMems/IntervalList.h -rw-r--r-- root/root 13712 2018-08-27 19:38 ./usr/include/libMems/Islands.h -rw-r--r-- root/root 1825 2018-08-27 19:38 ./usr/include/libMems/LCB.h -rw-r--r-- root/root 1416 2018-08-27 19:38 ./usr/include/libMems/MaskedMemHash.h -rw-r--r-- root/root 926 2018-08-27 19:38 ./usr/include/libMems/Match.h -rw-r--r-- root/root 13449 2018-08-27 19:38 ./usr/include/libMems/MatchFinder.h -rw-r--r-- root/root 4728 2018-08-27 19:38 ./usr/include/libMems/MatchHashEntry.h -rw-r--r-- root/root 22769 2018-08-27 19:38 ./usr/include/libMems/MatchList.h -rw-r--r-- root/root 4377 2018-08-27 19:38 ./usr/include/libMems/MatchProjectionAdapter.h -rw-r--r-- root/root 4016 2018-08-27 19:38 ./usr/include/libMems/Matrix.h -rw-r--r-- root/root 7182 2018-08-27 19:38 ./usr/include/libMems/MemHash.h -rw-r--r-- root/root 1543 2018-08-27 19:38 ./usr/include/libMems/Memory.h -rw-r--r-- root/root 1988 2018-08-27 19:38 ./usr/include/libMems/MemorySML.h -rw-r--r-- root/root 5235 2018-08-27 19:38 ./usr/include/libMems/MuscleInterface.h -rw-r--r-- root/root 4605 2018-08-27 19:38 ./usr/include/libMems/NumericMatrix.h -rw-r--r-- root/root 3674 2018-08-27 19:38 ./usr/include/libMems/PairwiseMatchAdapter.h -rw-r--r-- root/root 1013 2018-08-27 19:38 ./usr/include/libMems/PairwiseMatchFinder.h -rw-r--r-- root/root 10333 2018-08-27 19:38 ./usr/include/libMems/PhyloTree.h -rw-r--r-- root/root 24671 2018-08-27 19:38 ./usr/include/libMems/ProgressiveAligner.h -rw-r--r-- root/root 1428 2018-08-27 19:38 ./usr/include/libMems/RepeatHash.h -rw-r--r-- root/root 1453 2018-08-27 19:38 ./usr/include/libMems/RepeatMatch.h -rw-r--r-- root/root 2195 2018-08-27 19:38 ./usr/include/libMems/RepeatMatchList.h -rw-r--r-- root/root 10167 2018-08-27 19:38 ./usr/include/libMems/Scoring.h -rw-r--r-- root/root 9694 2018-08-27 19:38 ./usr/include/libMems/SeedMasks.h -rw-r--r-- root/root 2483 2018-08-27 19:38 ./usr/include/libMems/SeedOccurrenceList.h -rw-r--r-- root/root 4383 2018-08-27 19:38 ./usr/include/libMems/SlotAllocator.h -rw-r--r-- root/root 12250 2018-08-27 19:38 ./usr/include/libMems/SortedMerList.h -rw-r--r-- root/root 7625 2018-08-27 19:38 ./usr/include/libMems/SparseAbstractMatch.h -rw-r--r-- root/root 3100 2018-08-27 19:38 ./usr/include/libMems/SubstitutionMatrix.h -rw-r--r-- root/root 1879 2018-08-27 19:38 ./usr/include/libMems/SuperInterval.h -rw-r--r-- root/root 4590 2018-08-27 19:38 ./usr/include/libMems/TreeUtilities.h -rw-r--r-- root/root 7254 2018-08-27 19:38 ./usr/include/libMems/UngappedLocalAlignment.h -rw-r--r-- root/root 1214 2018-08-27 19:38 ./usr/include/libMems/configuration.h drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/include/libMems/dmSML/ -rw-r--r-- root/root 381 2018-08-27 19:38 ./usr/include/libMems/dmSML/aPOSIXaio.h -rw-r--r-- root/root 328 2018-08-27 19:38 ./usr/include/libMems/dmSML/alibc.h -rw-r--r-- root/root 387 2018-08-27 19:38 ./usr/include/libMems/dmSML/alinuxaio.h -rw-r--r-- root/root 4402 2018-08-27 19:38 ./usr/include/libMems/dmSML/asyncio.h -rw-r--r-- root/root 377 2018-08-27 19:38 ./usr/include/libMems/dmSML/awin32aio.h -rw-r--r-- root/root 7161 2018-08-27 19:38 ./usr/include/libMems/dmSML/buffer.h -rw-r--r-- root/root 4979 2018-08-27 19:38 ./usr/include/libMems/dmSML/dmsort.h -rw-r--r-- root/root 2197 2018-08-27 19:38 ./usr/include/libMems/dmSML/sml.h -rw-r--r-- root/root 2438 2018-08-27 19:38 ./usr/include/libMems/dmSML/sorting.h -rw-r--r-- root/root 393 2018-08-27 19:38 ./usr/include/libMems/dmSML/timing.h -rw-r--r-- root/root 731 2018-08-27 19:38 ./usr/include/libMems/dmSML/util.h -rw-r--r-- root/root 13038 2018-08-27 19:38 ./usr/include/libMems/gnAlignedSequences.h -rw-r--r-- root/root 7484 2018-08-27 19:38 ./usr/include/libMems/gnRAWSequence.h -rw-r--r-- root/root 309 2018-08-27 19:38 ./usr/include/libMems/twister.h drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/ -rw-r--r-- root/root 4254706 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/libMems.a lrwxrwxrwx root/root 0 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/libMems.so -> libMems.so.1.0.0 drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/pkgconfig/ -rw-r--r-- root/root 393 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libMems.pc drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/doc/libmems-dev/ -rw-r--r-- root/root 923 2018-08-27 19:38 ./usr/share/doc/libmems-dev/changelog.Debian.gz -rw-r--r-- root/root 2465 2018-08-27 19:38 ./usr/share/doc/libmems-dev/copyright libmems1-dbgsym_1.6.0+4725-8_armhf.deb -------------------------------------- new Debian package, version 2.0. size 10924332 bytes: control archive=552 bytes. 402 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libmems1-dbgsym Source: libmems Version: 1.6.0+4725-8 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 10975 Depends: libmems1 (= 1.6.0+4725-8) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libmems1 Build-Ids: 929f20966b7d54ce511f028ebffc8294cd08d9c2 drwxr-xr-x root/root 0 2018-08-27 19:38 ./ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/debug/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/debug/.build-id/92/ -rw-r--r-- root/root 11227828 2018-08-27 19:38 ./usr/lib/debug/.build-id/92/9f20966b7d54ce511f028ebffc8294cd08d9c2.debug drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-08-27 19:38 ./usr/share/doc/libmems1-dbgsym -> libmems1 libmems1_1.6.0+4725-8_armhf.deb ------------------------------- new Debian package, version 2.0. size 556004 bytes: control archive=1176 bytes. 1219 bytes, 24 lines control 223 bytes, 3 lines md5sums 19 bytes, 1 lines shlibs 65 bytes, 2 lines triggers Package: libmems1 Source: libmems Version: 1.6.0+4725-8 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1257 Depends: libboost-filesystem1.67.0, libboost-iostreams1.67.0, libc6 (>= 2.29), libgcc1 (>= 1:3.5), libgenome0, libmuscle1 (>= 3.7+4565), libstdc++6 (>= 9) Conflicts: libmems-1.6-1, libmems-1.6-1v5 Replaces: libmems-1.6-1, libmems-1.6-1v5 Section: libs Priority: optional Multi-Arch: same Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Description: library to support DNA string matching and comparative genomics libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements. . This package contains the dynamic library. drwxr-xr-x root/root 0 2018-08-27 19:38 ./ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/ lrwxrwxrwx root/root 0 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/libMems.so.1 -> libMems.so.1.0.0 -rw-r--r-- root/root 1271772 2018-08-27 19:38 ./usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-08-27 19:38 ./usr/share/doc/libmems1/ -rw-r--r-- root/root 923 2018-08-27 19:38 ./usr/share/doc/libmems1/changelog.Debian.gz -rw-r--r-- root/root 2465 2018-08-27 19:38 ./usr/share/doc/libmems1/copyright lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [592 B] Get:5 copy:/<>/apt_archive ./ Packages [680 B] Fetched 2235 B in 0s (177 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libperl4-corelibs-perl libauthen-sasl-perl libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded. 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http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.48.0 [1309 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9315 kB in 0s (42.0 MB/s) Selecting previously unselected package readline-common. 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Setting up lintian (2.48.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.29-9) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 282768 Build-Time: 563 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 25 Job: libmems_1.6.0+4725-8 Lintian: pass Machine Architecture: amd64 Package: libmems Package-Time: 600 Source-Version: 1.6.0+4725-8 Space: 282768 Status: successful Version: 1.6.0+4725-8 -------------------------------------------------------------------------------- Finished at 2020-02-01T18:22:19Z Build needed 00:10:00, 282768k disk space