sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | freebayes 1.3.6-1 (armel) Sun, 23 Jan 2022 21:19:31 +0000 | +==============================================================================+ Package: freebayes Version: 1.3.6-1 Source Version: 1.3.6-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-6f88fcfa-2516-4b99-93eb-788bb61adea2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-dNQJdd/resolver-2hZjla' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2022-01-23-2002.02-F-2022-01-23-0801.52.pdiff [36.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2022-01-23-2002.02-F-2022-01-23-0801.52.pdiff [46.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2022-01-23-2002.02-F-2022-01-23-0801.52.pdiff [36.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2022-01-23-2002.02-F-2022-01-23-0801.52.pdiff [46.8 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [8503 kB] Fetched 8879 kB in 4s (2328 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debianutils libgnutls30 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1478 kB of archives. After this operation, 3072 B disk space will be freed. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 debianutils amd64 5.7-0.1 [102 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libgnutls30 amd64 3.7.3-4 [1376 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1478 kB in 0s (54.4 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 ... 10584 files and directories currently installed.) Preparing to unpack .../debianutils_5.7-0.1_amd64.deb ... Unpacking debianutils (5.7-0.1) over (5.6-0.1) ... Setting up debianutils (5.7-0.1) ... (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 ... 10583 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.3-4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.3-4) over (3.7.3-3) ... Setting up libgnutls30:amd64 (3.7.3-4) ... Processing triggers for libc-bin (2.33-3) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'freebayes' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/freebayes.git Please use: git clone https://salsa.debian.org/med-team/freebayes.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2912 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main freebayes 1.3.6-1 (dsc) [2232 B] Get:2 http://debian.oregonstate.edu/debian unstable/main freebayes 1.3.6-1 (tar) [2898 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main freebayes 1.3.6-1 (diff) [11.4 kB] Fetched 2912 kB in 0s (68.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/freebayes-dNQJdd/freebayes-1.3.6' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-dNQJdd' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, debhelper, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, debhelper, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/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 [512 B] Get:5 copy:/<>/apt_archive ./ Packages [584 B] Fetched 2053 B in 0s (78.3 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc binutils-arm-linux-gnueabi bsdextrautils build-essential cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11 g++-11-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-arm-linux-gnueabi gcc-11-arm-linux-gnueabi-base gcc-11-base:armel gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.1:armel libbrotli1:armel libbwa-dev:armel libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libcurl4-gnutls-dev:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:armel libdeflate0:armel libdisorder-dev:armel libdisorder0:armel libdpkg-perl libelf1 libexpat1 libfastahack-dev:armel libfastahack0:armel libffi8:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfml-dev:armel libfml0:armel libgcc-11-dev-armel-cross libgcc-9-dev:armel libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libhogweed6:armel libhts-dev:armel libhts3:armel libhtscodecs2:armel libicu67 libidn2-0:armel libio-string-perl libjsoncpp-dev:armel libjsoncpp25:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libmpdec3 libncurses6:armel libnettle8:armel libnghttp2-14:armel libnsl-dev libnsl-dev:armel libnsl2:armel libp11-kit0:armel libperl5.32 libpipeline1 libpsl5:armel libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libseqlib-dev:armel libseqlib2:armel libsigsegv2 libsmithwaterman-dev:armel libsmithwaterman0:armel libsqlite3-0 libssh2-1:armel libssl1.1:armel libssw-dev:armel libssw0:armel libstdc++-11-dev libstdc++-11-dev-armel-cross libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtabixpp-dev:armel libtabixpp0:armel libtasn1-6:armel libtinfo6:armel libtirpc-dev libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libvcflib-dev:armel libvcflib1:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armel linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db media-types meson ninja-build perl perl-modules-5.32 pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal rpcsvc-proto samtools:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-11-multilib gcc-11-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc:armel glibc-doc:armel libc-l10n:armel locales:armel libnss-nis:armel libnss-nisplus:armel glibc-doc manpages-dev:armel libcurl4-doc:armel libgnutls28-dev:armel libidn11-dev:armel libkrb5-dev:armel libldap2-dev:armel librtmp-dev:armel libssh2-1-dev:armel gnupg git bzr gnutls-bin:armel krb5-doc:armel krb5-user:armel liblzma-doc:armel libstdc++-11-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools python3.9-venv python3.9-doc binfmt-support cwltool:armel Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx ca-certificates:armel libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales:armel libldap-common:armel libgpm2:armel publicsuffix:armel ca-certificates libsasl2-modules:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc binutils-arm-linux-gnueabi bsdextrautils build-essential cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11 g++-11-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-arm-linux-gnueabi gcc-11-arm-linux-gnueabi-base gcc-11-base:armel gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.1:armel libbrotli1:armel libbwa-dev:armel libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libcurl4-gnutls-dev:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:armel libdeflate0:armel libdisorder-dev:armel libdisorder0:armel libdpkg-perl libelf1 libexpat1 libfastahack-dev:armel libfastahack0:armel libffi8:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfml-dev:armel libfml0:armel libgcc-11-dev-armel-cross libgcc-9-dev:armel libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libhogweed6:armel libhts-dev:armel libhts3:armel libhtscodecs2:armel libicu67 libidn2-0:armel libio-string-perl libjsoncpp-dev:armel libjsoncpp25:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libmpdec3 libncurses6:armel libnettle8:armel libnghttp2-14:armel libnsl-dev libnsl-dev:armel libnsl2:armel libp11-kit0:armel libperl5.32 libpipeline1 libpsl5:armel libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libseqlib-dev:armel libseqlib2:armel libsigsegv2 libsmithwaterman-dev:armel libsmithwaterman0:armel libsqlite3-0 libssh2-1:armel libssl1.1:armel libssw-dev:armel libssw0:armel libstdc++-11-dev libstdc++-11-dev-armel-cross libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtabixpp-dev:armel libtabixpp0:armel libtasn1-6:armel libtinfo6:armel libtirpc-dev libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libvcflib-dev:armel libvcflib1:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armel linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db media-types meson ninja-build perl perl-modules-5.32 pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal rpcsvc-proto samtools:armel sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 183 newly installed, 0 to remove and 0 not upgraded. Need to get 252 MB of archives. After this operation, 897 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1004 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-6 [2824 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-6 [4106 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-6 [293 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-minimal amd64 3.9.10-1 [803 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.4.3-1 [106 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9-minimal amd64 3.9.10-1 [1937 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.9.8-1 [38.5 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 media-types all 5.0.0 [32.5 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.37.2-2 [822 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-stdlib amd64 3.9.10-1 [1683 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9 amd64 3.9.10-1 [487 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.9.8-1 [21.6 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.9.8-1 [38.1 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.4.0-4+b1 [200 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.41-2 [295 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.41-2 [129 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.41-2 [66.9 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-8 [936 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.2-6 [143 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.5-1 [37.6 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-4 [1354 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.5-1.1 [823 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 bc amd64 1.07.1-3+b1 [110 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.37.50.20220121-1 [3157 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.27-1.1 [118 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.33-3 [2276 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev amd64 11.2.0-14 [1979 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11 amd64 11.2.0-14 [10.2 MB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:11.2.0-2 [1636 B] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.21.1 [1568 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.21.1 [2171 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabi-base amd64 11.2.0-9cross1 [206 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [48.3 MB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:11.2.0-2 [17.0 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.33-1cross1 [1130 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 11.2.0-9cross1 [38.5 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 11.2.0-9cross1 [88.5 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 11.2.0-9cross1 [8812 B] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-armel-cross all 11.2.0-9cross1 [1937 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 11.2.0-9cross1 [426 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 11.2.0-9cross1 [798 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-11-dev-armel-cross all 11.2.0-9cross1 [703 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [54.8 MB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:11.2.0-2 [1460 B] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.15.5-1cross1 [1541 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.33-1cross1 [1810 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev-armel-cross all 11.2.0-9cross1 [1954 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [52.4 MB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:11.2.0-2 [1176 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.12+dfsg-5+b1 [701 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg-2 [340 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.9 [6704 B] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.6 [193 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.186-1 [179 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.6 [1054 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel gcc-11-base armel 11.2.0-14 [207 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 11.2.0-14 [38.4 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.33-3 [2363 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.4.0-4+b1 [2703 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 11.2.0-14 [9016 B] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 11.2.0-14 [467 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libbamtools2.5.1 armel 2.5.1+dfsg-10+b1 [134 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libbamtools-dev armel 2.5.1+dfsg-10+b1 [189 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel libbrotli1 armel 1.0.9-2+b3 [278 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libbwa-dev armel 0.7.17-6+b1 [137 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-5 [44.8 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.15.15-1 [1443 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.27-1.1 [97.3 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.27-1.1 [127 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armel libcom-err2 armel 1.46.5-2 [74.9 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libkrb5support0 armel 1.18.3-7 [62.4 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libk5crypto3 armel 1.18.3-7 [108 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libkeyutils1 armel 1.6.1-2 [14.5 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel libssl1.1 armel 1.1.1m-1 [1275 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel libkrb5-3 armel 1.18.3-7 [315 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armel libgssapi-krb5-2 armel 1.18.3-7 [142 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel libtirpc3 armel 1.3.2-2 [71.6 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libnsl2 armel 1.3.0-2 [33.0 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libtirpc-dev armel 1.3.2-2 [182 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armel libnsl-dev armel 1.3.0-2 [61.7 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.33-3 [1857 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armel libgmp10 armel 2:6.2.1+dfsg-3 [506 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armel libnettle8 armel 3.7.3-1 [281 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main armel libhogweed6 armel 3.7.3-1 [307 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main armel libunistring2 armel 0.9.10-6 [360 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armel libidn2-0 armel 2.3.2-2 [92.2 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armel libffi8 armel 3.4.2-4 [21.1 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main armel libp11-kit0 armel 0.24.0-6 [325 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main armel libtasn1-6 armel 4.18.0-4 [50.6 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main armel libgnutls30 armel 3.7.3-4 [1298 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main armel libdb5.3 armel 5.3.28+dfsg1-0.8 [572 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-modules-db armel 2.1.27+dfsg2-3 [72.8 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-2 armel 2.1.27+dfsg2-3 [103 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main armel libldap-2.4-2 armel 2.4.59+dfsg-1 [209 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main armel libnghttp2-14 armel 1.43.0-1 [65.5 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main armel libpsl5 armel 0.21.0-1.2 [56.2 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main armel librtmp1 armel 2.4+20151223.gitfa8646d.1-2+b2 [55.1 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main armel libssh2-1 armel 1.10.0-2 [162 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main armel libzstd1 armel 1.4.8+dfsg-3 [273 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main armel libcurl3-gnutls armel 7.81.0-1 [314 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main armel libcurl4-gnutls-dev armel 7.81.0-1 [415 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main armel libdeflate0 armel 1.9-1 [52.2 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main armel libdeflate-dev armel 1.9-1 [48.4 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main armel libdisorder0 armel 0.0.2+git20130809.8062ee1-4 [6236 B] Get:147 http://debian.oregonstate.edu/debian unstable/main armel libdisorder-dev armel 0.0.2+git20130809.8062ee1-4 [4524 B] Get:148 http://debian.oregonstate.edu/debian unstable/main armel libfastahack0 armel 1.0.0+dfsg-9 [23.7 kB] Get:149 http://debian.oregonstate.edu/debian unstable/main armel libfastahack-dev armel 1.0.0+dfsg-9 [27.7 kB] Get:150 http://debian.oregonstate.edu/debian unstable/main armel libfml0 armel 0.1+git20190320.b499514-1+b1 [70.0 kB] Get:151 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] Get:152 http://debian.oregonstate.edu/debian unstable/main armel libfml-dev armel 0.1+git20190320.b499514-1+b1 [80.7 kB] Get:153 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 11.2.0-14 [90.7 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 11.2.0-14 [799 kB] Get:155 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.4.0-4+b1 [640 kB] Get:156 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.70.2-1 [1403 kB] Get:157 http://debian.oregonstate.edu/debian unstable/main armel libhtscodecs2 armel 1.1.1-3+b1 [51.3 kB] Get:158 http://debian.oregonstate.edu/debian unstable/main armel liblzma5 armel 5.2.5-2 [159 kB] Get:159 http://debian.oregonstate.edu/debian unstable/main armel libhts3 armel 1.13+ds-2 [343 kB] Get:160 http://debian.oregonstate.edu/debian unstable/main armel liblzma-dev armel 5.2.5-2 [220 kB] Get:161 http://debian.oregonstate.edu/debian unstable/main armel libhts-dev armel 1.13+ds-2 [4051 kB] Get:162 http://debian.oregonstate.edu/debian unstable/main armel libjsoncpp25 armel 1.9.5-2 [66.4 kB] Get:163 http://debian.oregonstate.edu/debian unstable/main armel libjsoncpp-dev armel 1.9.5-2 [26.3 kB] Get:164 http://debian.oregonstate.edu/debian unstable/main armel libtinfo6 armel 6.3-2 [335 kB] Get:165 http://debian.oregonstate.edu/debian unstable/main armel libncurses6 armel 6.3-2 [81.7 kB] Get:166 http://debian.oregonstate.edu/debian unstable/main armel libssw0 armel 1.1-13 [20.9 kB] Get:167 http://debian.oregonstate.edu/debian unstable/main armel libseqlib2 armel 1.2.0+dfsg-8+b1 [132 kB] Get:168 http://debian.oregonstate.edu/debian unstable/main armel libssw-dev armel 1.1-13 [24.4 kB] Get:169 http://debian.oregonstate.edu/debian unstable/main armel libseqlib-dev armel 1.2.0+dfsg-8+b1 [204 kB] Get:170 http://debian.oregonstate.edu/debian unstable/main armel libsmithwaterman0 armel 0.0+git20160702.2610e25-12 [32.2 kB] Get:171 http://debian.oregonstate.edu/debian unstable/main armel libsmithwaterman-dev armel 0.0+git20160702.2610e25-12 [37.9 kB] Get:172 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.4.0-4+b1 [1761 kB] Get:173 http://debian.oregonstate.edu/debian unstable/main armel libtabixpp0 armel 1.1.0-6 [8672 B] Get:174 http://debian.oregonstate.edu/debian unstable/main armel libtabixpp-dev armel 1.1.0-6 [8276 B] Get:175 http://debian.oregonstate.edu/debian unstable/main armel libvcflib1 armel 1.0.2+dfsg-5 [135 kB] Get:176 http://debian.oregonstate.edu/debian unstable/main armel libvcflib-dev armel 1.0.2+dfsg-5 [85.2 kB] Get:177 http://debian.oregonstate.edu/debian unstable/main amd64 ninja-build amd64 1.10.1-1 [112 kB] Get:178 http://debian.oregonstate.edu/debian unstable/main amd64 python3-pkg-resources all 59.6.0-1.2 [196 kB] Get:179 http://debian.oregonstate.edu/debian unstable/main amd64 python3-lib2to3 all 3.9.10-1 [79.4 kB] Get:180 http://debian.oregonstate.edu/debian unstable/main amd64 python3-distutils all 3.9.10-1 [146 kB] Get:181 http://debian.oregonstate.edu/debian unstable/main amd64 meson all 0.61.1-1 [517 kB] Get:182 http://debian.oregonstate.edu/debian unstable/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get:183 http://debian.oregonstate.edu/debian unstable/main armel samtools armel 1.13-4 [540 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 252 MB in 2s (124 MB/s) Selecting previously unselected package perl-modules-5.32. (Reading database ... 10583 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-6_all.deb ... Unpacking perl-modules-5.32 (5.32.1-6) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../1-libperl5.32_5.32.1-6_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-6) ... Selecting previously unselected package perl. Preparing to unpack .../2-perl_5.32.1-6_amd64.deb ... Unpacking perl (5.32.1-6) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../3-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../4-libpython3.9-minimal_3.9.10-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.10-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../5-libexpat1_2.4.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.3-1) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../6-python3.9-minimal_3.9.10-1_amd64.deb ... Unpacking python3.9-minimal (3.9.10-1) ... Setting up libpython3.9-minimal:amd64 (3.9.10-1) ... Setting up libexpat1:amd64 (2.4.3-1) ... Setting up python3.9-minimal (3.9.10-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12848 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.8-1_amd64.deb ... Unpacking python3-minimal (3.9.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_5.0.0_all.deb ... Unpacking media-types (5.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-2_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-2) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../3-libsqlite3-0_3.37.2-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.37.2-2) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../4-libpython3.9-stdlib_3.9.10-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.10-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../5-python3.9_3.9.10-1_amd64.deb ... Unpacking python3.9 (3.9.10-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.9.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.8-1) ... Setting up python3-minimal (3.9.8-1) ... Selecting previously unselected package python3. (Reading database ... 13254 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.8-1_amd64.deb ... Unpacking python3 (3.9.8-1) ... Selecting previously unselected package gcc-9-base:armel. Preparing to unpack .../001-gcc-9-base_9.4.0-4+b1_armel.deb ... Unpacking gcc-9-base:armel (9.4.0-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.41-2_amd64.deb ... Unpacking libmagic-mgc (1:5.41-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../004-libmagic1_1%3a5.41-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-2) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.41-2_amd64.deb ... Unpacking file (1:5.41-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-8_amd64.deb ... Unpacking groff-base (1.22.4-8) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.37.2-6_amd64.deb ... Unpacking bsdextrautils (2.37.2-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.5-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.5-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.9.4-4_amd64.deb ... Unpacking man-db (2.9.4-4) ... Selecting previously unselected package ucf. Preparing to unpack .../012-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../013-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../168-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up media-types (5.0.0) ... Setting up libpipeline1:amd64 (1.5.5-1) ... Setting up gcc-11-base:armel (11.2.0-14) ... Setting up binutils-arm-linux-gnueabi (2.37.50.20220121-1) ... Setting up gcc-11-arm-linux-gnueabi-base:amd64 (11.2.0-9cross1) ... Setting up bsdextrautils (2.37.2-6) ... Setting up libicu67:amd64 (67.1-7) ... Setting up cpp-11-arm-linux-gnueabi (11.2.0-9cross1) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libglib2.0-0:amd64 (2.70.2-1) ... No schema files found: doing nothing. Setting up perl-modules-5.32 (5.32.1-6) ... Setting up libsqlite3-0:amd64 (3.37.2-2) ... Setting up libmagic1:amd64 (1:5.41-2) ... Setting up linux-libc-dev:armel (5.15.15-1) ... Setting up bc (1.07.1-3+b1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.41-2) ... Setting up ninja-build (1.10.1-1) ... Setting up linux-libc-dev-armel-cross (5.15.5-1cross1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up cpp-arm-linux-gnueabi (4:11.2.0-2) ... Setting up rpcsvc-proto (1.4.2-4) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libperl5.32:amd64 (5.32.1-6) ... Setting up libbwa-dev:armel (0.7.17-6+b1) ... Setting up libc6-armel-cross (2.33-1cross1) ... Setting up gcc-11-cross-base (11.2.0-9cross1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:amd64 (1:4.4.27-1.1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libc6-dev:amd64 (2.33-3) ... Setting up libc6-dev-armel-cross (2.33-1cross1) ... Setting up libelf1:amd64 (0.186-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5+b1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:amd64 (3.9.10-1) ... Setting up libpython3-stdlib:amd64 (3.9.8-1) ... Setting up gcc-9-base:armel (9.4.0-4+b1) ... Setting up gettext (0.21-4) ... Setting up libgomp1-armel-cross (11.2.0-9cross1) ... Setting up libtool (2.4.6-15) ... Setting up libgcc-s1-armel-cross (11.2.0-9cross1) ... Setting up m4 (1.4.18-5) ... Setting up libstdc++6-armel-cross (11.2.0-9cross1) ... Setting up libatomic1-armel-cross (11.2.0-9cross1) ... Setting up perl (5.32.1-6) ... Setting up libubsan1-armel-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up libdpkg-perl (1.21.1) ... Setting up autoconf (2.71-2) ... Setting up libstdc++-11-dev:amd64 (11.2.0-14) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-8) ... Setting up libsub-override-perl (0.09-2) ... Setting up python3.9 (3.9.10-1) ... Setting up libasan6-armel-cross (11.2.0-9cross1) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up libgcc-11-dev-armel-cross (11.2.0-9cross1) ... Setting up g++-11 (11.2.0-14) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.6) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up python3 (3.9.8-1) ... Setting up man-db (2.9.4-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.21.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dh-autoreconf (20) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up pkg-config (0.29.2-1) ... Setting up g++ (4:11.2.0-2) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libstdc++-11-dev-armel-cross (11.2.0-9cross1) ... Setting up build-essential (12.9) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up python3-lib2to3 (3.9.10-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.9.10-1) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up gcc-11-arm-linux-gnueabi (11.2.0-9cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up meson (0.61.1-1) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... 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 g++-11-arm-linux-gnueabi (11.2.0-9cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg-2) ... 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 dh-strip-nondeterminism (1.13.0-1) ... Setting up gcc-arm-linux-gnueabi (4:11.2.0-2) ... Setting up debhelper (13.6) ... Setting up g++-arm-linux-gnueabi (4:11.2.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-armel (12.9) ... Setting up libgcc-s1:armel (11.2.0-14) ... Setting up libc6:armel (2.33-3) ... Setting up libffi8:armel (3.4.2-4) ... Setting up libtasn1-6:armel (4.18.0-4) ... Setting up libbz2-1.0:armel (1.0.8-5) ... Setting up libdb5.3:armel (5.3.28+dfsg1-0.8) ... Setting up libstdc++6:armel (11.2.0-14) ... Setting up libtinfo6:armel (6.3-2) ... Setting up libhtscodecs2:armel (1.1.1-3+b1) ... Setting up libdisorder0:armel (0.0.2+git20130809.8062ee1-4) ... Setting up libzstd1:armel (1.4.8+dfsg-3) ... Setting up libkeyutils1:armel (1.6.1-2) ... Setting up liblzma5:armel (5.2.5-2) ... Setting up libssl1.1:armel (1.1.1m-1) ... Setting up libbrotli1:armel (1.0.9-2+b3) ... Setting up libsmithwaterman0:armel (0.0+git20160702.2610e25-12) ... Setting up libnghttp2-14:armel (1.43.0-1) ... Setting up libunistring2:armel (0.9.10-6) ... Setting up libdeflate0:armel (1.9-1) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libcrypt1:armel (1:4.4.27-1.1) ... Setting up libidn2-0:armel (2.3.2-2) ... Setting up libcom-err2:armel (1.46.5-2) ... Setting up libgomp1:armel (11.2.0-14) ... Setting up libfastahack0:armel (1.0.0+dfsg-9) ... Setting up libkrb5support0:armel (1.18.3-7) ... Setting up libsasl2-modules-db:armel (2.1.27+dfsg2-3) ... Setting up libfastahack-dev:armel (1.0.0+dfsg-9) ... Setting up libasan5:armel (9.4.0-4+b1) ... Setting up libnettle8:armel (3.7.3-1) ... Setting up libgmp10:armel (2:6.2.1+dfsg-3) ... Setting up libncurses6:armel (6.3-2) ... Setting up libp11-kit0:armel (0.24.0-6) ... Setting up libbamtools2.5.1:armel (2.5.1+dfsg-10+b1) ... Setting up libatomic1:armel (11.2.0-14) ... Setting up libjsoncpp25:armel (1.9.5-2) ... Setting up libk5crypto3:armel (1.18.3-7) ... Setting up libdisorder-dev:armel (0.0.2+git20130809.8062ee1-4) ... Setting up libsasl2-2:armel (2.1.27+dfsg2-3) ... Setting up liblzma-dev:armel (5.2.5-2) ... Setting up libubsan1:armel (11.2.0-14) ... Setting up libcrypt-dev:armel (1:4.4.27-1.1) ... Setting up libssh2-1:armel (1.10.0-2) ... Setting up libkrb5-3:armel (1.18.3-7) ... Setting up libdeflate-dev:armel (1.9-1) ... Setting up libssw0:armel (1.1-13) ... Setting up libjsoncpp-dev:armel (1.9.5-2) ... Setting up libpsl5:armel (0.21.0-1.2) ... Setting up libhogweed6:armel (3.7.3-1) ... Setting up libssw-dev:armel (1.1-13) ... Setting up libfml0:armel (0.1+git20190320.b499514-1+b1) ... Setting up libgcc-9-dev:armel (9.4.0-4+b1) ... Setting up libgnutls30:armel (3.7.3-4) ... Setting up librtmp1:armel (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libbamtools-dev:armel (2.5.1+dfsg-10+b1) ... Setting up libgssapi-krb5-2:armel (1.18.3-7) ... Setting up libsmithwaterman-dev:armel (0.0+git20160702.2610e25-12) ... Setting up libtirpc3:armel (1.3.2-2) ... Setting up libldap-2.4-2:armel (2.4.59+dfsg-1) ... Setting up libcurl3-gnutls:armel (7.81.0-1) ... Setting up libcurl4-gnutls-dev:armel (7.81.0-1) ... Setting up libtirpc-dev:armel (1.3.2-2) ... Setting up libnsl2:armel (1.3.0-2) ... Setting up libhts3:armel (1.13+ds-2) ... Setting up samtools:armel (1.13-4) ... Setting up libnsl-dev:armel (1.3.0-2) ... Setting up libtabixpp0:armel (1.1.0-6) ... Setting up libc6-dev:armel (2.33-3) ... Setting up libseqlib2:armel (1.2.0+dfsg-8+b1) ... Setting up libstdc++-9-dev:armel (9.4.0-4+b1) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up libvcflib1:armel (1.0.2+dfsg-5) ... Setting up libfml-dev:armel (0.1+git20190320.b499514-1+b1) ... Setting up libhts-dev:armel (1.13+ds-2) ... Setting up libseqlib-dev:armel (1.2.0+dfsg-8+b1) ... Setting up libtabixpp-dev:armel (1.1.0-6) ... Setting up libvcflib-dev:armel (1.0.2+dfsg-5) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.33-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64) Toolchain package versions: binutils_2.37.50.20220121-1 dpkg-dev_1.21.1 g++-11_11.2.0-14 gcc-11_11.2.0-14 libc6-dev_2.33-3 libstdc++-11-dev_11.2.0-14 libstdc++-11-dev-armel-cross_11.2.0-9cross1 libstdc++-9-dev_9.4.0-4+b1 libstdc++6_11.2.0-14 libstdc++6-armel-cross_11.2.0-9cross1 linux-libc-dev_5.15.15-1 Package versions: adduser_3.118 apt_2.3.14 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12.2 base-passwd_3.5.52 bash_5.1-6 bc_1.07.1-3+b1 binutils_2.37.50.20220121-1 binutils-arm-linux-gnueabi_2.37.50.20220121-1 binutils-common_2.37.50.20220121-1 binutils-x86-64-linux-gnu_2.37.50.20220121-1 bsdextrautils_2.37.2-6 bsdutils_1:2.37.2-6 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-14 cpp-11-arm-linux-gnueabi_11.2.0-9cross1 cpp-8_8.4.0-7 cpp-arm-linux-gnueabi_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-armel_12.9 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.6 debian-archive-keyring_2021.1.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dpkg_1.21.1 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.27-1 fdisk_2.37.2-6 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-14 g++-11-arm-linux-gnueabi_11.2.0-9cross1 g++-arm-linux-gnueabi_4:11.2.0-2 gcc_4:11.2.0-2 gcc-10-base_10.3.0-14 gcc-11_11.2.0-14 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media-types_5.0.0 meson_0.61.1-1 mount_2.37.2-6 ncurses-base_6.3-2 ncurses-bin_6.3-2 ninja-build_1.10.1-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.28_5.28.1-6 perl-modules-5.32_5.32.1-6 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.9.8-1 python3-distutils_3.9.10-1 python3-lib2to3_3.9.10-1 python3-minimal_3.9.8-1 python3-pkg-resources_59.6.0-1.2 python3.9_3.9.10-1 python3.9-minimal_3.9.10-1 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 samtools_1.13-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-6 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freebayes Binary: freebayes Architecture: any Version: 1.3.6-1 Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/freebayes Vcs-Git: https://salsa.debian.org/med-team/freebayes.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel , libvcflib-tools , debhelper Package-List: freebayes deb science optional arch=any Checksums-Sha1: 2513323e336e02b5cc83d43c9f5b725579c0b75a 2898209 freebayes_1.3.6.orig.tar.gz d1d72a14f9b82132767886cd8a7b9b02ae22159f 11384 freebayes_1.3.6-1.debian.tar.xz Checksums-Sha256: d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 2898209 freebayes_1.3.6.orig.tar.gz 23a4950fcaab4971df38d8c100ec4c0c4055e7a599c0a3823f1fe26e8a78a566 11384 freebayes_1.3.6-1.debian.tar.xz Files: e8fe2bf8bb0139bb313744e5fb8e4105 2898209 freebayes_1.3.6.orig.tar.gz fcded594e43cf8f9a0b18748deff21b8 11384 freebayes_1.3.6-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHqleIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFjpw//ctTpgtIx+4PFIK2hNTXGLALlvFmRurk/ sM2nRNWF+V4rAN8RLxxO7ftey2cKsUa+LH2nI2HQWEB2ijPpj6AEie8SmZxg5oJl ap+zxR1eanLQlyo17d/WYFOCJZ5fBkXlMZgRTAWe8bV0+/bE2g6WZsZW21p9yKd2 kNJB/gNQfdOtcg58soYKTkxHwN/S69qxWU6SiLRH/zqSdXcG9nGhliLJkt2xoQe8 u8rUYl6zHTGdmR8tLTymeV6bj/O9pAIM39nhji3XeI0HEQDqzFplHeh1r7VKukim EoQ6zOjnum4m4524zOfHUS5G4kPOxUPmMhcbWStdDl+TvjfHKXISbGxnSYmABgPG RIPFhEkxR8Td4NnOhcVmjaX65A0gytf1fpywJh//aqRrxURITHR4+43nqAAyZg8d sE+Uvs1Tjo5u9WZtJJsFNpHAyLhUKNTVi5ExMhVp5og0wga6IXJr3yJAmkrHHqFG XSrLZrJz6qZfb00ifnojk/Hx2yOUPeOJ9swnjsJW09pGe0uhMgQ9MdDIOPRXVM5D ajvbvVvxgIq8moa7IegAaPsKH7G8+mhltmxVVQY56a3R52VPPngbrT186HBSBks2 jovEV/a7oiTByZkt9S7TdooNttkDumWsqHIkT1/lNyE7y4ONoRnJF9oywKyG8Ben 7Ai8uTZcDe0= =LkxN -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.rggoOdOm/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 21 11:15:46 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./freebayes_1.3.6-1.dsc dpkg-source: info: extracting freebayes in /<> dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.6-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-6f88fcfa-2516-4b99-93eb-788bb61adea2 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary-arch dh binary-arch --buildsystem=meson --builddir=build dh_update_autotools_config -a -O--buildsystem=meson -O--builddir=build dh_autoreconf -a -O--buildsystem=meson -O--builddir=build dh_auto_configure -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabi --cross-file /<>/debian/.debhelper/generated/_source/meson-cross-file.conf DEPRECATION: c_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: cpp_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: c_link_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: cpp_link_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. The Meson build system Version: 0.61.1 Source dir: /<> Build dir: /<>/build Build type: cross build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: /usr/bin/arm-linux-gnueabi-gcc (gcc 11.2.0 "arm-linux-gnueabi-gcc (Debian 11.2.0-9) 11.2.0") C linker for the host machine: /usr/bin/arm-linux-gnueabi-gcc ld.bfd 2.37.50.20220121 C++ compiler for the host machine: /usr/bin/arm-linux-gnueabi-g++ (gcc 11.2.0 "arm-linux-gnueabi-g++ (Debian 11.2.0-9) 11.2.0") C++ linker for the host machine: /usr/bin/arm-linux-gnueabi-g++ ld.bfd 2.37.50.20220121 C compiler for the build machine: cc (gcc 11.2.0 "cc (Debian 11.2.0-14) 11.2.0") C linker for the build machine: cc ld.bfd 2.37.50.20220121 C++ compiler for the build machine: c++ (gcc 11.2.0 "c++ (Debian 11.2.0-14) 11.2.0") C++ linker for the build machine: c++ ld.bfd 2.37.50.20220121 Build machine cpu family: x86_64 Build machine cpu: x86_64 Host machine cpu family: arm Host machine cpu: armel Target machine cpu family: arm Target machine cpu: armel Found pkg-config: /usr/bin/arm-linux-gnueabi-pkg-config (0.29.2) Run-time dependency zlib found: YES 1.2.11 Run-time dependency liblzma found: YES 5.2.5 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.13+ds Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 freebayes 1.3.6 User defined options Cross files : /<>/debian/.debhelper/generated/_source/meson-cross-file.conf buildtype : plain libdir : lib/arm-linux-gnueabi localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j1 -v [1/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp ../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] 160 | switch (this->type) { | ^ ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Allele.h:8, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Allele.h:8, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&, bool (*)(Allele&, Allele&))’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::__cxx11::list&, bool (*)(Allele&, Allele&))’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector alleleUnion(std::vector&, std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Allele.h:8, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleleGroups(std::vector >&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleles(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleles(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleleGroups(std::vector >&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/map:60, from ../src/Allele.h:10, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Allele.h:10, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘std::map countAlleles(std::__cxx11::list&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Allele.h:8, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector uniqueAlleles(std::__cxx11::list&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Allele.h:10, from ../src/Allele.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [2/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 813 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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 = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In member function ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:340:5: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 340 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:356:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 356 | _M_realloc_insert(begin() + __n, std::move(__v)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1646 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In member function ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1646 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘std::vector AlleleParser::genotypeAlleles(std::map, std::vector >&, Samples&, bool, int)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 1294 | { return _M_insert_rval(__position, std::move(__x)); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/AlleleParser.h:11, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/AlleleParser.h:7, from ../src/AlleleParser.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 1294 | { return _M_insert_rval(__position, std::move(__x)); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void AlleleParser::updateInputVariants(long int, int)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [3/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [4/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Bias.h:8, from ../src/Bias.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Bias.h:8, from ../src/Bias.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void Bias::open(std::string&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [5/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [6/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [7/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/DataLikelihood.h:5, from ../src/DataLikelihood.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector > probObservedAllelesGivenGenotypes(Sample&, std::vector&, Bias&, std::vector&, Contamination&, std::map, double>&, Parameters&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/bits/vector.tcc: In function ‘void calculateSampleDataLikelihoods(Samples&, Results&, AlleleParser*, std::map >&, Parameters&, bool, Bias&, std::vector&, Contamination&, std::map, double>&, std::map, std::vector > >&, std::map, std::vector > >&, std::map, std::vector > >&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [8/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Dirichlet.h:4, from ../src/Dirichlet.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double dirichletln(const std::vector&, const std::vector&, long double)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double dirichlet(const std::vector&, const std::vector&, long double)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [9/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [10/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algobase.h:71, from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:63, from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/FBFasta.h:12, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/predefined_ops.h: In function ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator >; _Iterator2 = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)]’: /usr/arm-linux-gnueabi/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/FBFasta.h:15, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FB::FastaIndexEntry&}; _Tp = FB::FastaIndexEntry; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/FBFasta.h:12, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, FB::FastaIndexEntry>; _KeyOfValue = std::_Select1st, FB::FastaIndexEntry> >; _Compare = std::less >; _Alloc = std::allocator, FB::FastaIndexEntry> >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FB::FastaIndexEntry>, std::_Select1st, FB::FastaIndexEntry> >, std::less >, std::allocator, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/FBFasta.h:12, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In member function ‘std::string FB::FastaReference::sequenceNameStartingWith(std::string)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FB::FastaIndexEntry>, std::_Select1st, FB::FastaIndexEntry> >, std::less >, std::allocator, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/FBFasta.h:18, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/FBFasta.h:18, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FB::FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:231:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 231 | if (__comp(__first + __secondChild, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 232 | __first + (__secondChild - 1))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/FBFasta.h:18, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1642 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1648:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1648 | if (__comp(__i, __first)) | ~~~~~~^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:82:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 82 | if (__comp(__a, __b)) | ~~~~~~^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:84:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 86 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:91:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 91 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 93 | else if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1917 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/FBFasta.h:12, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘std::ostream& FB::operator<<(std::ostream&, FB::FastaIndex&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FB::FastaIndexEntry>, std::_Select1st, FB::FastaIndexEntry> >, std::less >, std::allocator, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/FBFasta.h:15, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/FBFasta.h:18, from ../src/FBFasta.cpp:9: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [11/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘std::vector Genotype::alternateAlleles(std::string&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘long double GenotypeCombo::hweExpectedFrequencyln(Genotype*)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘std::vector Genotype::alleleProbabilities()’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘std::vector GenotypeCombo::alleleProbs()’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘std::vector Genotype::alleleProbabilities(Bias&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/vector:67, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘std::vector > multichoose(int, std::vector&) [with T = Allele]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/Genotype.h:10, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Genotype.h:10, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘void addAllHomozygousCombos(std::__cxx11::list&, SampleDataLikelihoods&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::vector&, long double, bool, bool, bool, bool, bool, bool, long double)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/Genotype.h:10, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Genotype.h:10, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘void combinePopulationCombos(std::__cxx11::list&, std::map, std::__cxx11::list >&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1646 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In constructor ‘Genotype::Genotype(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘std::vector allPossibleGenotypes(int, std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1646 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Genotype.h:10, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘std::vector > alternateAlleles(GenotypeCombo&, std::string)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Genotype.h:5, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginals(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void sortSampleDataLikelihoods(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Genotype.h:7, from ../src/Genotype.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [12/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [13/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [14/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Marginals.h:4, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/Marginals.h:5, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Genotype*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Marginals.h:5, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In function ‘long double marginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Marginals.h:4, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Marginals.h:5, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Marginals.h:4, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In function ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Marginals.h:5, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/Marginals.h:4, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Marginals.h:5, from ../src/Marginals.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [15/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Utility.h:7, from ../src/Multinomial.h:4, from ../src/Multinomial.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double multinomialSamplingProb(const std::vector&, const std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double multinomialSamplingProbLn(const std::vector&, const std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [16/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/set:60, from ../src/NonCall.h:6, from ../src/NonCall.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, NonCall>; _KeyOfValue = std::_Select1st, NonCall> >; _Compare = std::less >; _Alloc = std::allocator, NonCall> >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/NonCall.h:7, from ../src/NonCall.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In member function ‘void NonCalls::aggregatePerSample(std::map, NonCall>&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h: In member function ‘void NonCalls::record(const string&, long int, const Samples&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [17/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [18/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Result.h:6, from ../src/Result.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Result.h:6, from ../src/Result.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../src/Result.h:6, from ../src/Result.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/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-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In member function ‘void Result::sortDataLikelihoods()’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [19/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/ResultData.h:4, from ../src/ResultData.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:60, from ../src/Genotype.h:10, from ../src/ResultData.h:7, from ../src/ResultData.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/ResultData.h:4, from ../src/ResultData.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector&, std::map, int>, int, std::vector >&, int, GenotypeCombo&, std::map, std::vector >&, std::map, std::vector >&, std::map >&, std::map >&, std::vector >&, AlleleParser*)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/map:61, from ../src/Genotype.h:10, from ../src/ResultData.h:7, from ../src/ResultData.cpp:1: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [20/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [21/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [22/27] /usr/bin/arm-linux-gnueabi-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Utility.h:7, from ../src/Utility.cpp:3: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double jointQuality(const std::vector&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘double entropy(const string&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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 ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Exp(const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:326:10, inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25: ../ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big ttmath::Big::operator+(const ttmath::Big&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../ttmath/ttmathuint.h:2740:43: warning: ‘maxNb.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big ttmath::Big::operator+(const ttmath::Big&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../ttmath/ttmathuint.h:2740:43: warning: ‘maxNb.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In file included from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with unsigned int argument_size = 8; unsigned int value_size = 8]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with unsigned int argument_size = 8; unsigned int value_size = 8]’ at ../ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with unsigned int value_size = 8]’ at ../ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big ttmath::Big::operator+(const ttmath::Big&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:5570:15, inlined from ‘long double logsumexp_probs(const std::vector&)’ at ../src/Utility.cpp:381:48: ../ttmath/ttmathint.h:652:61: warning: ‘maxNb.ttmath::Big<8, 2>::exponent.ttmath::Int<8>::.ttmath::UInt<8>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/Utility.h:7, from ../src/Utility.cpp:3: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘long double poissonPvalLn(int, int)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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 ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with unsigned int value_size = 2]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<8, 2>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [23/27] /usr/bin/arm-linux-gnueabi-g++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [24/27] rm -f libfreebayes_common.a && /usr/bin/arm-linux-gnueabi-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [25/27] /usr/bin/arm-linux-gnueabi-g++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SampleDataLikelihood&}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/list:63, from ../src/Utility.h:8, from ../src/Parameters.h:14, from ../src/freebayes.cpp:26: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list::iterator’ changed in GCC 7.1 1909 | _M_insert(iterator __position, _Args&&... __args) | ^~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/vector:67, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h: In member function ‘void Results::update(SampleDataLikelihoods&)’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In function ‘int main(int, char**)’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: 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-gnueabi/include/c++/11/vector:67, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/list:63, from ../src/Utility.h:8, from ../src/Parameters.h:14, from ../src/freebayes.cpp:26: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:67, from ../src/freebayes.cpp:12: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/list:63, from ../src/Utility.h:8, from ../src/Parameters.h:14, from ../src/freebayes.cpp:26: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ [26/27] /usr/bin/arm-linux-gnueabi-g++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabi/libz.so /usr/lib/arm-linux-gnueabi/liblzma.so -pthread /usr/lib/arm-linux-gnueabi/libhts.so /usr/lib/arm-linux-gnueabi/libtabixpp.so /usr/lib/arm-linux-gnueabi/libvcflib.so /usr/lib/arm-linux-gnueabi/libsmithwaterman.so /usr/lib/arm-linux-gnueabi/libdisorder.so /usr/lib/arm-linux-gnueabi/libfastahack.so /usr/lib/arm-linux-gnueabi/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group [27/27] /usr/bin/arm-linux-gnueabi-g++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabi/libz.so /usr/lib/arm-linux-gnueabi/liblzma.so -pthread /usr/lib/arm-linux-gnueabi/libhts.so /usr/lib/arm-linux-gnueabi/libvcflib.so /usr/lib/arm-linux-gnueabi/libsmithwaterman.so /usr/lib/arm-linux-gnueabi/libdisorder.so /usr/lib/arm-linux-gnueabi/libfastahack.so /usr/lib/arm-linux-gnueabi/libseqlib.so /usr/lib/libbwa.a /usr/lib/arm-linux-gnueabi/libtabixpp.so -Wl,--end-group create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson -O--builddir=build dh_prep -a -O--buildsystem=meson -O--builddir=build dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/<>/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /<>/debian/freebayes/usr/bin Installing bamleftalign to /<>/debian/freebayes/usr/bin dh_installdocs -a -O--buildsystem=meson -O--builddir=build dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build dh_installexamples -a -O--buildsystem=meson -O--builddir=build dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build dh_perl -a -O--buildsystem=meson -O--builddir=build dh_link -a -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build dh_compress -a -O--buildsystem=meson -O--builddir=build dh_fixperms -a -O--buildsystem=meson -O--builddir=build dh_missing -a -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dpkg-shlibdeps: warning: debian/freebayes/usr/bin/freebayes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/freebayes/usr/bin/bamleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--buildsystem=meson -O--builddir=build dh_gencontrol -a -O--buildsystem=meson -O--builddir=build dh_md5sums -a -O--buildsystem=meson -O--builddir=build dh_builddeb -a -O--buildsystem=meson -O--builddir=build dpkg-deb: building package 'freebayes' in '../freebayes_1.3.6-1_armel.deb'. dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.6-1_armel.deb'. dpkg-genbuildinfo --build=any -O../freebayes_1.3.6-1_armel.buildinfo dpkg-genchanges --build=any -O../freebayes_1.3.6-1_armel.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-01-23T21:22:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.6-1_armel.changes: -------------------------------- Format: 1.8 Date: Fri, 21 Jan 2022 12:09:32 +0100 Source: freebayes Binary: freebayes freebayes-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 1.3.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.6-1) unstable; urgency=medium . * New upstream version * Add missing build dependency on dh addon. 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+------------------------------------------------------------------------------+ Format: 1.0 Source: freebayes Binary: freebayes freebayes-dbgsym Architecture: armel Version: 1.3.6-1 Checksums-Md5: 5919f0b8455765aaede54cee69471e45 6470260 freebayes-dbgsym_1.3.6-1_armel.deb b7fdad27897b74ee8b9353c1a087ac9e 1396632 freebayes_1.3.6-1_armel.deb Checksums-Sha1: 09b5b83ac445f9a57b56ee7e87b0489980f49b02 6470260 freebayes-dbgsym_1.3.6-1_armel.deb 2eebfaf250b802819482322f294e44d13eb29ac2 1396632 freebayes_1.3.6-1_armel.deb Checksums-Sha256: 3c279d488c1d7c203362ef24b8827240e8e546889906a40548605c0a1f3cdb9c 6470260 freebayes-dbgsym_1.3.6-1_armel.deb 1ef30a69372c067a876911dd7bd282cf9c0cefc40e7e0b35e444ded6aad69757 1396632 freebayes_1.3.6-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 23 Jan 2022 21:22:26 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12.2), base-passwd (= 3.5.52), bash (= 5.1-6), bc (= 1.07.1-3+b1), binutils (= 2.37.50.20220121-1), binutils-common (= 2.37.50.20220121-1), binutils-x86-64-linux-gnu (= 2.37.50.20220121-1), bsdextrautils (= 2.37.2-6), bsdutils (= 1:2.37.2-6), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-14), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.6), debianutils (= 5.7-0.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.7-5), dpkg (= 1.21.1), dpkg-dev (= 1.21.1), dwz (= 0.14-1), file (= 1:5.41-2), findutils (= 4.8.0-1), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-14), gcc (= 4:11.2.0-2), gcc-11 (= 11.2.0-14), gcc-11-base (= 11.2.0-14), gettext (= 0.21-4), gettext-base (= 0.21-4), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.10-4), hostname (= 3.23), init-system-helpers (= 1.61), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-14), libatomic1 (= 11.2.0-14), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.6-1), libaudit1 (= 1:3.0.6-1+b1), libbamtools-dev (= 2.5.1+dfsg-10+b1), libbamtools2.5.1 (= 2.5.1+dfsg-10+b1), libbinutils (= 2.37.50.20220121-1), libblkid1 (= 2.37.2-6), libbrotli1 (= 1.0.9-2+b3), libbwa-dev (= 0.7.17-6+b1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.33-3), libc-dev-bin (= 2.33-3), libc6 (= 2.33-3), libc6-dev (= 2.33-3), libcap-ng0 (= 0.7.9-2.2+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 11.2.0-14), libcom-err2 (= 1.46.5-2), libcrypt-dev (= 1:4.4.27-1.1), libcrypt1 (= 1:4.4.27-1.1), libctf-nobfd0 (= 2.37.50.20220121-1), libctf0 (= 2.37.50.20220121-1), libcurl3-gnutls (= 7.81.0-1), libcurl4-gnutls-dev (= 7.81.0-1), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.261), libdebhelper-perl (= 13.6), libdeflate-dev (= 1.9-1), libdeflate0 (= 1.9-1), libdisorder-dev (= 0.0.2+git20130809.8062ee1-4), libdisorder0 (= 0.0.2+git20130809.8062ee1-4), libdpkg-perl (= 1.21.1), libelf1 (= 0.186-1), libexpat1 (= 2.4.3-1), libfastahack-dev (= 1.0.0+dfsg-9), libfastahack0 (= 1.0.0+dfsg-9), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libfml-dev (= 0.1+git20190320.b499514-1+b1), libfml0 (= 0.1+git20190320.b499514-1+b1), libgcc-11-dev (= 11.2.0-14), libgcc-s1 (= 11.2.0-14), libgcrypt20 (= 1.9.4-5), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libglib2.0-0 (= 2.70.2-1), libgmp10 (= 2:6.2.1+dfsg-3), libgnutls30 (= 3.7.3-4), libgomp1 (= 11.2.0-14), libgpg-error0 (= 1.43-3), libgssapi-krb5-2 (= 1.18.3-7), libhogweed6 (= 3.7.3-1), libhts-dev (= 1.13+ds-2), libhts3 (= 1.13+ds-2), libhtscodecs2 (= 1.1.1-3+b1), libicu67 (= 67.1-7), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-14), libjsoncpp-dev (= 1.9.5-2), libjsoncpp25 (= 1.9.5-2), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), libldap-2.4-2 (= 2.4.59+dfsg-1), liblsan0 (= 11.2.0-14), liblz4-1 (= 1.9.3-2), liblzma-dev (= 5.2.5-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmount1 (= 2.37.2-6), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.3-2), libncursesw6 (= 6.3-2), libnettle8 (= 3.7.3-1), libnghttp2-14 (= 1.43.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libp11-kit0 (= 0.24.0-6), libpam-modules (= 1.4.0-11), libpam-modules-bin (= 1.4.0-11), libpam-runtime (= 1.4.0-11), libpam0g (= 1.4.0-11), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.5-1), libpsl5 (= 0.21.0-1.2), libpython3-stdlib (= 3.9.8-1), libpython3.9-minimal (= 3.9.10-1), libpython3.9-stdlib (= 3.9.10-1), libquadmath0 (= 11.2.0-14), libreadline8 (= 8.1.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.27+dfsg2-3), libsasl2-modules-db (= 2.1.27+dfsg2-3), libseccomp2 (= 2.5.3-2), libselinux1 (= 3.3-1+b1), libseqlib-dev (= 1.2.0+dfsg-8+b1), libseqlib2 (= 1.2.0+dfsg-8+b1), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.37.2-6), libsmithwaterman-dev (= 0.0+git20160702.2610e25-12), libsmithwaterman0 (= 0.0+git20160702.2610e25-12), libsqlite3-0 (= 3.37.2-2), libssh2-1 (= 1.10.0-2), libssl1.1 (= 1.1.1m-1), libssw-dev (= 1.1-13), libssw0 (= 1.1-13), libstdc++-11-dev (= 11.2.0-14), libstdc++6 (= 11.2.0-14), libsub-override-perl (= 0.09-2), libsystemd0 (= 250.3-1), libtabixpp-dev (= 1.1.0-6), libtabixpp0 (= 1.1.0-6), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3-2), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-14), libubsan1 (= 11.2.0-14), libuchardet0 (= 0.0.7-1), libudev1 (= 250.3-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-6), libvcflib-dev (= 1.0.2+dfsg-5), libvcflib1 (= 1.0.2+dfsg-5), libxml2 (= 2.9.12+dfsg-5+b1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.15-1), login (= 1:4.8.1-2), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-4), mawk (= 1.3.4.20200120-2), media-types (= 5.0.0), meson (= 0.61.1-1), ncurses-base (= 6.3-2), ncurses-bin (= 6.3-2), ninja-build (= 1.10.1-1), patch (= 2.7.6-7), perl (= 5.32.1-6), perl-base (= 5.32.1-6), perl-modules-5.32 (= 5.32.1-6), pkg-config (= 0.29.2-1), po-debconf (= 1.0.21+nmu1), python3 (= 3.9.8-1), python3-distutils (= 3.9.10-1), python3-lib2to3 (= 3.9.10-1), python3-minimal (= 3.9.8-1), python3-pkg-resources (= 59.6.0-1.2), python3.9 (= 3.9.10-1), python3.9-minimal (= 3.9.10-1), readline-common (= 8.1.2-1), rpcsvc-proto (= 1.4.2-4), samtools (= 1.13-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1), tar (= 1.34+dfsg-1), tzdata (= 2021e-1), util-linux (= 2.37.2-6), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) 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="1642763372" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes-dbgsym_1.3.6-1_armel.deb ---------------------------------- new Debian package, version 2.0. size 6470260 bytes: control archive=640 bytes. 420 bytes, 12 lines control 299 bytes, 3 lines md5sums Package: freebayes-dbgsym Source: freebayes Version: 1.3.6-1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 6536 Depends: freebayes (= 1.3.6-1) Section: debug Priority: optional Description: debug symbols for freebayes Build-Ids: c2e65aed01a83ba10b9b3235852139ba424d74a7 ddb47325dfec28914a75d1f75b7ee29f956d03a2 drwxr-xr-x root/root 0 2022-01-21 11:09 ./ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/.build-id/c2/ -rw-r--r-- root/root 604152 2022-01-21 11:09 ./usr/lib/debug/.build-id/c2/e65aed01a83ba10b9b3235852139ba424d74a7.debug drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/.build-id/dd/ -rw-r--r-- root/root 5783020 2022-01-21 11:09 ./usr/lib/debug/.build-id/dd/b47325dfec28914a75d1f75b7ee29f956d03a2.debug drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/lib/debug/.dwz/arm-linux-gnueabi/ -rw-r--r-- root/root 291764 2022-01-21 11:09 ./usr/lib/debug/.dwz/arm-linux-gnueabi/freebayes.debug drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-01-21 11:09 ./usr/share/doc/freebayes-dbgsym -> freebayes freebayes_1.3.6-1_armel.deb --------------------------- new Debian package, version 2.0. size 1396632 bytes: control archive=2224 bytes. 851 bytes, 17 lines control 4632 bytes, 55 lines md5sums Package: freebayes Version: 1.3.6-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 3727 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libseqlib2 (>= 1.2.0+dfsg), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.2+dfsg), zlib1g (>= 1:1.1.4) Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2022-01-21 11:09 ./ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/bin/ -rwxr-xr-x root/root 1150152 2022-01-21 11:09 ./usr/bin/bamleftalign -rwxr-xr-x root/root 1748112 2022-01-21 11:09 ./usr/bin/freebayes drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/doc/freebayes/ -rw-r--r-- root/root 10293 2022-01-21 09:38 ./usr/share/doc/freebayes/README.md.gz -rw-r--r-- root/root 278 2022-01-21 11:09 ./usr/share/doc/freebayes/README.test -rw-r--r-- root/root 83 2022-01-21 11:09 ./usr/share/doc/freebayes/README.test_data -rw-r--r-- root/root 3317 2022-01-21 09:38 ./usr/share/doc/freebayes/RELEASE-NOTES.md -rw-r--r-- root/root 1833 2022-01-21 11:09 ./usr/share/doc/freebayes/changelog.Debian.gz -rw-r--r-- root/root 3194 2022-01-21 11:09 ./usr/share/doc/freebayes/copyright drwxr-xr-x root/root 0 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/ -rw-r--r-- root/root 83 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/README.test_data drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/bash-tap/ -rw-r--r-- root/root 109 2022-01-21 09:38 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./usr/share/doc/freebayes/examples/splice/1:883884-887618.bam.bai -rw-r--r-- root/root 3801 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa -rw-r--r-- root/root 15 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa.fai drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/ -rw-r--r-- root/root 3648 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/00_region_and_target_handling.t -rw-r--r-- root/root 4908 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/01_call_variants.t -rw-r--r-- root/root 2947 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/01b_call_variants.t -rw-r--r-- root/root 2943 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/02_multi_bam.t -rw-r--r-- root/root 1488 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/03_reference_bases.t -rw-r--r-- root/root 246 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/targets.bed drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/test-simple-bash/ -rw-r--r-- root/root 17 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.alt -rw-r--r-- root/root 230 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.bam -rw-r--r-- root/root 96 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.bam.bai -rw-r--r-- root/root 112 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.bed -rw-r--r-- root/root 17 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.ref -rw-r--r-- root/root 15 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.ref.fai -rw-r--r-- root/root 550 2022-01-21 11:09 ./usr/share/doc/freebayes/examples/test.vcf drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/ -rw-r--r-- root/root 636 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/1read.bam -rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/1read.bam.bai -rw-r--r-- root/root 287213 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam -rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam.bai -rw-r--r-- root/root 155615 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.cram -rw-r--r-- root/root 16307 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.giab.vcf -rw-r--r-- root/root 287228 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam -rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam.bai -rw-r--r-- root/root 12581 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.fa -rw-r--r-- root/root 33 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.fa.fai -rw-r--r-- root/root 2394 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.vcf.gz -rw-r--r-- root/root 120 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.vcf.gz.tbi -rw-r--r-- 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./usr/share/doc/freebayes/run-unit-test.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/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 [644 B] Get:5 copy:/<>/apt_archive ./ Packages [715 B] Fetched 2322 B in 0s (87.3 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 libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:armel t1utils unzip 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 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1.002005-1 [11.6 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.005004-3 [60.5 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libmouse-perl amd64 2.5.10-1+b1 [172 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.122-1 [56.0 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b7 [17.4 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.009-1 [11.8 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.634-1 [46.5 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1+b1 [99.3 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1+b1 [103 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.21-1 [50.8 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.26-1 [28.7 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-1+b2 [27.8 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b8 [8724 B] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.13-1 [13.2 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-1 [197 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b3 [75.8 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b2 [20.3 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 5.10-1 [91.0 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.83+ds-1 [35.5 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.22-5 [88.3 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-26 [171 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.114.0 [1382 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6751 kB in 0s (30.0 MB/s) Selecting previously unselected package diffstat. (Reading database ... 23010 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../01-libassuan0_2.5.5-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-3_amd64.deb ... Unpacking gpgconf (2.2.27-3) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-3_amd64.deb ... Unpacking gpg (2.2.27-3) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../04-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../05-libapt-pkg-perl_0.1.40_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. 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Unpacking libconfig-tiny-perl (2.28-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../22-libparams-util-perl_1.102-1+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-1+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../23-libsub-install-perl_0.928-1.1_all.deb ... Unpacking libsub-install-perl (0.928-1.1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../24-libdata-optlist-perl_0.112-1_all.deb ... Unpacking libdata-optlist-perl (0.112-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../25-libsub-exporter-perl_0.988-1_all.deb ... Unpacking libsub-exporter-perl (0.988-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../26-libconst-fast-perl_0.014-1.1_all.deb ... Unpacking libconst-fast-perl (0.014-1.1) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../27-libcpanel-json-xs-perl_4.27-1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.27-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../28-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../29-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../30-libiterator-perl_0.03+ds1-1.1_all.deb ... Unpacking libiterator-perl (0.03+ds1-1.1) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../31-libiterator-util-perl_0.02+ds1-1.1_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-1.1) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../32-libexporter-tiny-perl_1.002002-1_all.deb ... 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Selecting previously unselected package libstrictures-perl. Preparing to unpack .../66-libstrictures-perl_2.000006-1_all.deb ... Unpacking libstrictures-perl (2.000006-1) ... Selecting previously unselected package libmoox-aliases-perl. Preparing to unpack .../67-libmoox-aliases-perl_0.001006-1.1_all.deb ... Unpacking libmoox-aliases-perl (0.001006-1.1) ... Selecting previously unselected package libmouse-perl. Preparing to unpack .../68-libmouse-perl_2.5.10-1+b1_amd64.deb ... Unpacking libmouse-perl (2.5.10-1+b1) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../69-libpackage-stash-perl_0.39-1_all.deb ... Unpacking libpackage-stash-perl (0.39-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../70-libsub-identify-perl_0.14-1+b3_amd64.deb ... Unpacking libsub-identify-perl (0.14-1+b3) ... Selecting previously unselected package libsub-name-perl. 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Unpacking libproc-processtable-perl:amd64 (0.634-1) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../77-libsereal-decoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-decoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../78-libsereal-encoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-encoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../79-libsort-versions-perl_1.62-1_all.deb ... Unpacking libsort-versions-perl (1.62-1) ... Selecting previously unselected package libxs-parse-keyword-perl. Preparing to unpack .../80-libxs-parse-keyword-perl_0.21-1_amd64.deb ... Unpacking libxs-parse-keyword-perl (0.21-1) ... Selecting previously unselected package libsyntax-keyword-try-perl. Preparing to unpack .../81-libsyntax-keyword-try-perl_0.26-1_amd64.deb ... Unpacking libsyntax-keyword-try-perl (0.26-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../82-libterm-readkey-perl_2.38-1+b2_amd64.deb ... Unpacking libterm-readkey-perl (2.38-1+b2) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../83-libtext-levenshteinxs-perl_0.03-4+b8_amd64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-4+b8) ... Selecting previously unselected package libtext-markdown-discount-perl:amd64. Preparing to unpack .../84-libtext-markdown-discount-perl_0.13-1_amd64.deb ... Unpacking libtext-markdown-discount-perl:amd64 (0.13-1) ... Selecting previously unselected package libtext-xslate-perl:amd64. Preparing to unpack .../85-libtext-xslate-perl_3.5.9-1_amd64.deb ... Unpacking libtext-xslate-perl:amd64 (3.5.9-1) ... Selecting previously unselected package libtime-duration-perl. Preparing to unpack .../86-libtime-duration-perl_1.21-1_all.deb ... 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Setting up lzip (1.22-5) ... update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-1+b3) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up liblist-moreutils-xs-perl (0.430-2) ... Setting up libparams-util-perl (1.102-1+b1) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b1) ... Setting up libsyntax-keyword-try-perl (0.26-1) ... 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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: 84868 Build-Time: 117 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 44 Job: freebayes_1.3.6-1 Lintian: pass Machine Architecture: amd64 Package: freebayes Package-Time: 175 Source-Version: 1.3.6-1 Space: 84868 Status: successful Version: 1.3.6-1 -------------------------------------------------------------------------------- Finished at 2022-01-23T21:22:26Z Build needed 00:02:55, 84868k disk space