https://launchpad.net/ubuntu/+archive/test-rebuild-20181222/+build/16069574 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-032 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_167 python-lpbuildd_167 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 25 Feb 09:37:05 ntpdate[1826]: adjust time server 10.211.37.1 offset -0.082789 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16069574 --image-type chroot /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-16069574 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16069574 Starting target for build PACKAGEBUILD-16069574 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16069574 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-16069574 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16069574 Updating target for build PACKAGEBUILD-16069574 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [88.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [88.7 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [968 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8269 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/multiverse armhf Packages [129 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main armhf Packages [180 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main Translation-en [101 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-security/universe armhf Packages [123 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-security/universe Translation-en [71.2 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/multiverse armhf Packages [1448 B] Get:14 http://ftpmaster.internal/ubuntu bionic-security/multiverse Translation-en [1848 B] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main armhf Packages [415 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main Translation-en [196 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/restricted armhf Packages [6476 B] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/restricted Translation-en [3076 B] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/universe armhf Packages [588 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/universe Translation-en [189 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/multiverse armhf Packages [3360 B] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/multiverse Translation-en [3452 B] Fetched 17.1 MB in 7s (2460 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils cpp cpp-7 dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libkmod2 libmount1 libncurses5 libncursesw5 libperl5.26 libpng16-16 libprocps6 libsmartcols1 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pkgbinarymangler procps systemd systemd-sysv tar tzdata ubuntu-keyring util-linux 74 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 44.4 MB of archives. After this operation, 233 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic-updates/main armhf base-files armhf 10.1ubuntu2.4 [59.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-updates/main armhf bsdutils armhf 1:2.31.1-0.4ubuntu3.3 [55.5 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates/main armhf tar armhf 1.29b-2ubuntu0.1 [209 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-updates/main armhf dpkg armhf 1.19.0.5ubuntu2.1 [1094 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libext2fs2 armhf 1.44.1-1ubuntu1.1 [144 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main armhf e2fsprogs armhf 1.44.1-1ubuntu1.1 [369 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ncurses-bin armhf 6.1-1ubuntu1.18.04 [155 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main armhf libperl5.26 armhf 5.26.1-6ubuntu0.3 [2888 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl armhf 5.26.1-6ubuntu0.3 [201 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl-base armhf 5.26.1-6ubuntu0.3 [1291 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl-modules-5.26 all 5.26.1-6ubuntu0.3 [2763 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libuuid1 armhf 2.31.1-0.4ubuntu3.3 [19.5 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libblkid1 armhf 2.31.1-0.4ubuntu3.3 [112 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libfdisk1 armhf 2.31.1-0.4ubuntu3.3 [152 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libmount1 armhf 2.31.1-0.4ubuntu3.3 [122 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libncurses5 armhf 6.1-1ubuntu1.18.04 [74.8 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libtinfo5 armhf 6.1-1ubuntu1.18.04 [68.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libncursesw5 armhf 6.1-1ubuntu1.18.04 [95.3 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libsmartcols1 armhf 2.31.1-0.4ubuntu3.3 [74.6 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/main armhf fdisk armhf 2.31.1-0.4ubuntu3.3 [97.5 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/main armhf util-linux armhf 2.31.1-0.4ubuntu3.3 [845 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ncurses-base all 6.1-1ubuntu1.18.04 [17.8 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libgomp1 armhf 8.2.0-1ubuntu2~18.04 [66.6 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-updates/main armhf gcc-8-base armhf 8.2.0-1ubuntu2~18.04 [18.4 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libgcc1 armhf 1:8.2.0-1ubuntu2~18.04 [37.1 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcc1-0 armhf 8.2.0-1ubuntu2~18.04 [32.7 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libatomic1 armhf 8.2.0-1ubuntu2~18.04 [7064 B] Get:28 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libstdc++6 armhf 8.2.0-1ubuntu2~18.04 [350 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-security/main armhf libudev1 armhf 237-3ubuntu10.13 [48.7 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libapt-pkg5.0 armhf 1.6.8 [731 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-security/main armhf libgcrypt20 armhf 1.8.1-4ubuntu1.1 [364 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpgv armhf 2.2.4-1ubuntu1.2 [167 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ubuntu-keyring all 2018.09.18.1~18.04.0 [22.4 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-updates/main armhf apt armhf 1.6.8 [1121 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-security/main armhf libapparmor1 armhf 2.12-4ubuntu5.1 [27.1 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu1.1 [119 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libkmod2 armhf 24-1ubuntu3.2 [34.3 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-updates/main armhf mount armhf 2.31.1-0.4ubuntu3.3 [99.7 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-security/main armhf libprocps6 armhf 2:3.3.12-3ubuntu1.1 [28.8 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-security/main armhf procps armhf 2:3.3.12-3ubuntu1.1 [213 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-security/main armhf systemd armhf 237-3ubuntu10.13 [2726 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-security/main armhf libsystemd0 armhf 237-3ubuntu10.13 [186 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-security/main armhf systemd-sysv armhf 237-3ubuntu10.13 [12.0 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcom-err2 armhf 1.44.1-1ubuntu1.1 [8416 B] Get:45 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libss2 armhf 1.44.1-1ubuntu1.1 [9392 B] Get:46 http://ftpmaster.internal/ubuntu bionic-security/main armhf libssl1.1 armhf 1.1.0g-2ubuntu4.3 [914 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-security/main armhf openssl armhf 1.1.0g-2ubuntu4.3 [509 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-security/main armhf tzdata all 2018i-0ubuntu0.18.04 [189 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-security/main armhf libpng16-16 armhf 1.6.34-1ubuntu0.18.04.1 [159 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils-arm-linux-gnueabihf armhf 2.30-21ubuntu1~18.04 [2175 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libbinutils armhf 2.30-21ubuntu1~18.04 [308 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils armhf 2.30-21ubuntu1~18.04 [3356 B] Get:53 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils-common armhf 2.30-21ubuntu1~18.04 [193 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libubsan0 armhf 7.3.0-27ubuntu1~18.04 [108 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libasan4 armhf 7.3.0-27ubuntu1~18.04 [327 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcilkrts5 armhf 7.3.0-27ubuntu1~18.04 [36.0 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-updates/main armhf g++-7 armhf 7.3.0-27ubuntu1~18.04 [6047 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-updates/main armhf gcc-7 armhf 7.3.0-27ubuntu1~18.04 [5951 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libstdc++-7-dev armhf 7.3.0-27ubuntu1~18.04 [1536 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libgcc-7-dev armhf 7.3.0-27ubuntu1~18.04 [706 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-updates/main armhf cpp-7 armhf 7.3.0-27ubuntu1~18.04 [5295 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-updates/main armhf gcc-7-base armhf 7.3.0-27ubuntu1~18.04 [19.0 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-updates/main armhf cpp armhf 4:7.3.0-3ubuntu2.1 [27.6 kB] Get:64 http://ftpmaster.internal/ubuntu bionic-updates/main armhf dpkg-dev all 1.19.0.5ubuntu2.1 [608 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libdpkg-perl all 1.19.0.5ubuntu2.1 [211 kB] Get:66 http://ftpmaster.internal/ubuntu bionic-updates/main armhf e2fslibs armhf 1.44.1-1ubuntu1.1 [2712 B] Get:67 http://ftpmaster.internal/ubuntu bionic-updates/main armhf gcc armhf 4:7.3.0-3ubuntu2.1 [5204 B] Get:68 http://ftpmaster.internal/ubuntu bionic-updates/main armhf g++ armhf 4:7.3.0-3ubuntu2.1 [1576 B] Get:69 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpg armhf 2.2.4-1ubuntu1.2 [408 kB] Get:70 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpgconf armhf 2.2.4-1ubuntu1.2 [105 kB] Get:71 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpg-agent armhf 2.2.4-1ubuntu1.2 [188 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcomerr2 armhf 1.44.1-1ubuntu1.1 [2712 B] Get:73 http://ftpmaster.internal/ubuntu bionic-security/main armhf linux-libc-dev armhf 4.15.0-45.48 [981 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-security/main armhf pkgbinarymangler all 138.18.04.0 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.4 MB in 2s (21.2 MB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu2.4_armhf.deb ... Unpacking base-files (10.1ubuntu2.4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu2.4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.31.1-0.4ubuntu3.3_armhf.deb ... Unpacking bsdutils (1:2.31.1-0.4ubuntu3.3) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.31.1-0.4ubuntu3.3) ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../tar_1.29b-2ubuntu0.1_armhf.deb ... Unpacking tar (1.29b-2ubuntu0.1) over (1.29b-2) ... Setting up tar (1.29b-2ubuntu0.1) ... (Reading database ... 12380 files and directories currently installed.) 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Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:armhf (5.26.1-6ubuntu0.3) ... Setting up libssl1.1:armhf (1.1.0g-2ubuntu4.3) ... Setting up openssl (1.1.0g-2ubuntu4.3) ... Setting up libcomerr2:armhf (1.44.1-1ubuntu1.1) ... Setting up gpg (2.2.4-1ubuntu1.2) ... Setting up libasan4:armhf (7.3.0-27ubuntu1~18.04) ... Setting up libbinutils:armhf (2.30-21ubuntu1~18.04) ... Setting up libcilkrts5:armhf (7.3.0-27ubuntu1~18.04) ... Setting up libubsan0:armhf (7.3.0-27ubuntu1~18.04) ... Setting up binutils-arm-linux-gnueabihf (2.30-21ubuntu1~18.04) ... Setting up libgcc-7-dev:armhf (7.3.0-27ubuntu1~18.04) ... Setting up cpp-7 (7.3.0-27ubuntu1~18.04) ... Setting up libstdc++-7-dev:armhf (7.3.0-27ubuntu1~18.04) ... Setting up perl (5.26.1-6ubuntu0.3) ... Setting up binutils (2.30-21ubuntu1~18.04) ... Setting up cpp (4:7.3.0-3ubuntu2.1) ... Setting up gcc-7 (7.3.0-27ubuntu1~18.04) ... Setting up g++-7 (7.3.0-27ubuntu1~18.04) ... Setting up libdpkg-perl (1.19.0.5ubuntu2.1) ... Setting up gcc (4:7.3.0-3ubuntu2.1) ... Setting up dpkg-dev (1.19.0.5ubuntu2.1) ... Setting up g++ (4:7.3.0-3ubuntu2.1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16069574 armhf bionic -c chroot:build-PACKAGEBUILD-16069574 --arch=armhf --dist=bionic --nolog pbbam_0.7.4+ds-1build2.dsc Initiating build PACKAGEBUILD-16069574 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-032.buildd +==============================================================================+ | pbbam 0.7.4+ds-1build2 (armhf) 25 Feb 2019 09:37 | +==============================================================================+ Package: pbbam Version: 0.7.4+ds-1build2 Source Version: 0.7.4+ds-1build2 Distribution: bionic Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/pbbam-j0wxqe/pbbam-0.7.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-j0wxqe' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16069574/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_0.7.4+ds-1build2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-FDpKEI/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-FDpKEI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FDpKEI/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-FDpKEI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FDpKEI/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-FDpKEI/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (126 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-FDpKEI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12385 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools Filtered Build-Depends: debhelper (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-QRuukm/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. Ign:1 copy:/<>/resolver-QRuukm/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QRuukm/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-QRuukm/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QRuukm/apt_archive ./ Sources [264 B] Get:5 copy:/<>/resolver-QRuukm/apt_archive ./ Packages [584 B] Fetched 2967 B in 0s (101 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install pbbam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.65-dev libbsd0 libcroco3 libcurl3-gnutls libcurl4 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.65-doc libboost-atomic1.65-dev libboost-chrono1.65-dev libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-date-time1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-iostreams1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-regex1.65-dev libboost-serialization1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-system1.65-dev libboost-test1.65-dev libboost-thread1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libssl-doc libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.65-dev libbsd0 libcroco3 libcurl3-gnutls libcurl4 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-pbbam-dummy zlib1g-dev 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 35.6 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 copy:/<>/resolver-QRuukm/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [916 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf libbsd0 armhf 0.8.7-1 [40.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf bsdmainutils armhf 11.1.2ubuntu1 [177 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main armhf man-db armhf 2.8.3-2ubuntu0.1 [993 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf liblzo2-2 armhf 2.08-1.2 [44.2 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main armhf libpython2.7-minimal armhf 2.7.15~rc1-1ubuntu0.1 [334 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main armhf python2.7-minimal armhf 2.7.15~rc1-1ubuntu0.1 [1082 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf python-minimal armhf 2.7.15~rc1-1 [28.1 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libexpat1 armhf 2.2.5-3 [59.7 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/main armhf libpython2.7-stdlib armhf 2.7.15~rc1-1ubuntu0.1 [1834 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-security/main armhf python2.7 armhf 2.7.15~rc1-1ubuntu0.1 [238 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libpython-stdlib armhf 2.7.15~rc1-1 [7624 B] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf python armhf 2.7.15~rc1-1 [140 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-security/main armhf libmagic-mgc armhf 1:5.32-2ubuntu0.1 [184 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-security/main armhf libmagic1 armhf 1:5.32-2ubuntu0.1 [62.7 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-security/main armhf file armhf 1:5.32-2ubuntu0.1 [21.5 kB] Get:20 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http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libldap-common all 2.4.45+dfsg-1ubuntu1.1 [16.6 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1ubuntu1.1 [132 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libnghttp2-14 armhf 1.30.0-1ubuntu1 [67.4 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [49.1 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-security/main armhf libcurl4 armhf 7.58.0-2ubuntu3.6 [183 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf libjsoncpp1 armhf 1.7.4-3 [65.9 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf librhash0 armhf 1.3.6-2 [90.3 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libuv1 armhf 1.18.0-3 [53.5 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf cmake armhf 3.10.2-1ubuntu2 [2721 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libtool all 2.4.6-2 [194 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main armhf dh-autoreconf all 17 [15.8 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-security/main armhf libarchive-zip-perl all 1.60-1ubuntu0.1 [84.6 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main armhf libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-security/main armhf gettext armhf 0.19.8.1-6ubuntu0.1 [834 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB] Get:68 http://ftpmaster.internal/ubuntu bionic-updates/main armhf debhelper all 11.1.6ubuntu2 [902 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf libboost1.65-dev armhf 1.65.1+dfsg-0ubuntu5 [7218 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf libboost-dev armhf 1.65.1.0ubuntu1 [3128 B] Get:71 http://ftpmaster.internal/ubuntu bionic-security/main armhf libcurl3-gnutls armhf 7.58.0-2ubuntu3.6 [182 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/universe armhf libhts2 armhf 1.7-2 [257 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf liblzma-dev armhf 5.2.2-1.3 [138 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/universe armhf libhts-dev armhf 1.7-2 [339 kB] Get:75 http://ftpmaster.internal/ubuntu bionic-security/main armhf libssl-dev armhf 1.1.0g-2ubuntu4.3 [1184 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/universe armhf python-cram all 0.7-1 [16.7 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/universe armhf samtools armhf 1.7-1 [257 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main armhf dh-exec armhf 0.23build1 [23.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.6 MB in 1s (27.3 MB/s) Selecting previously unselected package libbsd0:armhf. (Reading database ... 12385 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_armhf.deb ... Unpacking libbsd0:armhf (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu1_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_armhf.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2ubuntu0.1_armhf.deb ... Unpacking man-db (2.8.3-2ubuntu0.1) ... Selecting previously unselected package liblzo2-2:armhf. Preparing to unpack .../05-liblzo2-2_2.08-1.2_armhf.deb ... Unpacking liblzo2-2:armhf (2.08-1.2) ... 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Setting up libssl-dev:armhf (1.1.0g-2ubuntu4.3) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.56.3-0ubuntu0.18.04.1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6ubuntu0.1) ... Setting up cmake-data (3.10.2-1ubuntu2) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up libroken18-heimdal:armhf (7.5.0+dfsg-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armhf (0.8.7-1) ... Setting up libkrb5support0:armhf (1.16-2ubuntu0.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1.2) ... Setting up libmagic-mgc (1:5.32-2ubuntu0.1) ... Setting up libmagic1:armhf (1:5.32-2ubuntu0.1) ... Setting up librhash0:armhf (1.3.6-2) ... Setting up libcroco3:armhf (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-1) ... Setting up liblzma-dev:armhf (5.2.2-1.3) ... Setting up libkeyutils1:armhf (1.5.9-9.2ubuntu2) ... Setting up bsdmainutils (11.1.2ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libboost1.65-dev:armhf (1.65.1+dfsg-0ubuntu5) ... Setting up libpython2.7-stdlib:armhf (2.7.15~rc1-1ubuntu0.1) ... Setting up autopoint (0.19.8.1-6ubuntu0.1) ... Setting up liblzo2-2:armhf (2.08-1.2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up libjsoncpp1:armhf (1.7.4-3) ... Setting up libk5crypto3:armhf (1.16-2ubuntu0.1) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up gettext (0.19.8.1-6ubuntu0.1) ... Setting up libarchive13:armhf (3.2.2-3.1ubuntu0.3) ... Setting up libasn1-8-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libhcrypto4-heimdal:armhf (7.5.0+dfsg-1) ... Setting up python2.7 (2.7.15~rc1-1ubuntu0.1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2ubuntu0.1) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libpython-stdlib:armhf (2.7.15~rc1-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2ubuntu0.1) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:armhf (1.16-2ubuntu0.1) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libboost-dev:armhf (1.65.1.0ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up python (2.7.15~rc1-1) ... Setting up libtool (2.4.6-2) ... Setting up python-cram (0.7-1) ... Setting up po-debconf (1.0.20) ... Setting up libgssapi-krb5-2:armhf (1.16-2ubuntu0.1) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libldap-2.4-2:armhf (2.4.45+dfsg-1ubuntu1.1) ... Setting up libcurl3-gnutls:armhf (7.58.0-2ubuntu3.6) ... Setting up libcurl4:armhf (7.58.0-2ubuntu3.6) ... Setting up cmake (3.10.2-1ubuntu2) ... Setting up libhts2:armhf (1.7-2) ... Setting up libhts-dev:armhf (1.7-2) ... Setting up samtools (1.7-1) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu2) ... Setting up dh-autoreconf (17) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-21ubuntu1~18.04 dpkg-dev_1.19.0.5ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc-7_7.3.0-27ubuntu1~18.04 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 linux-libc-dev_4.15.0-45.48 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.8 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6ubuntu0.1 autotools-dev_20180224.1 base-files_10.1ubuntu2.4 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 binutils_2.30-21ubuntu1~18.04 binutils-arm-linux-gnueabihf_2.30-21ubuntu1~18.04 binutils-common_2.30-21ubuntu1~18.04 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3.3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 cmake_3.10.2-1ubuntu2 cmake-data_3.10.2-1ubuntu2 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2.1 cpp-7_7.3.0-27ubuntu1~18.04 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu2 debianutils_4.8.4 dh-autoreconf_17 dh-exec_0.23build1 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2.1 dpkg-dev_1.19.0.5ubuntu2.1 e2fslibs_1.44.1-1ubuntu1.1 e2fsprogs_1.44.1-1ubuntu1.1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3.3 file_1:5.32-2ubuntu0.1 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc_4:7.3.0-3ubuntu2.1 gcc-7_7.3.0-27ubuntu1~18.04 gcc-7-base_7.3.0-27ubuntu1~18.04 gcc-8-base_8.2.0-1ubuntu2~18.04 gettext_0.19.8.1-6ubuntu0.1 gettext-base_0.19.8.1-6ubuntu0.1 gpg_2.2.4-1ubuntu1.2 gpg-agent_2.2.4-1ubuntu1.2 gpgconf_2.2.4-1ubuntu1.2 gpgv_2.2.4-1ubuntu1.2 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5.1 libapt-pkg5.0_1.6.8 libarchive-zip-perl_1.60-1ubuntu0.1 libarchive13_3.2.2-3.1ubuntu0.3 libargon2-0_0~20161029-1.1 libasan4_7.3.0-27ubuntu1~18.04 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8.2.0-1ubuntu2~18.04 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-21ubuntu1~18.04 libblkid1_2.31.1-0.4ubuntu3.3 libboost-dev_1.65.1.0ubuntu1 libboost1.65-dev_1.65.1+dfsg-0ubuntu5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-1ubuntu2~18.04 libcilkrts5_7.3.0-27ubuntu1~18.04 libcom-err2_1.44.1-1ubuntu1.1 libcomerr2_1.44.1-1ubuntu1.1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1.1 libcurl3-gnutls_7.58.0-2ubuntu3.6 libcurl4_7.58.0-2ubuntu3.6 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2.1 libexpat1_2.2.5-3 libext2fs2_1.44.1-1ubuntu1.1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-27ubuntu1~18.04 libgcc1_1:8.2.0-1ubuntu2~18.04 libgcrypt20_1.8.1-4ubuntu1.1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.3-0ubuntu0.18.04.1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-1ubuntu2~18.04 libgpg-error0_1.27-6 libgssapi-krb5-2_1.16-2ubuntu0.1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2ubuntu0.1 libkeyutils1_1.5.9-9.2ubuntu2 libkmod2_24-1ubuntu3.2 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2ubuntu0.1 libkrb5support0_1.16-2ubuntu0.1 libldap-2.4-2_2.4.45+dfsg-1ubuntu1.1 libldap-common_2.4.45+dfsg-1ubuntu1.1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.32-2ubuntu0.1 libmagic1_1:5.32-2ubuntu0.1 libmount1_2.31.1-0.4ubuntu3.3 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1ubuntu1.18.04 libncursesw5_6.1-1ubuntu1.18.04 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6ubuntu0.3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1ubuntu0.18.04.1 libprocps6_2:3.3.12-3ubuntu1.1 libpsl5_0.19.1-5build1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15~rc1-1ubuntu0.1 libpython2.7-stdlib_2.7.15~rc1-1ubuntu0.1 libreadline7_7.0-3 librhash0_1.3.6-2 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3.3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1ubuntu1.1 libssl-dev_1.1.0g-2ubuntu4.3 libssl1.1_1.1.0g-2ubuntu4.3 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 libsystemd0_237-3ubuntu10.13 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1.18.04 libtool_2.4.6-2 libubsan0_7.3.0-27ubuntu1~18.04 libudev1_237-3ubuntu10.13 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libuuid1_2.31.1-0.4ubuntu3.3 libuv1_1.18.0-3 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1.2 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-45.48 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2ubuntu0.1 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.31.1-0.4ubuntu3.3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1.18.04 ncurses-bin_6.1-1ubuntu1.18.04 openssl_1.1.0g-2ubuntu4.3 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6ubuntu0.3 perl-base_5.26.1-6ubuntu0.3 perl-modules-5.26_5.26.1-6ubuntu0.3 pinentry-curses_1.1.0-1 pkgbinarymangler_138.18.04.0 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1.1 python_2.7.15~rc1-1 python-cram_0.7-1 python-minimal_2.7.15~rc1-1 python2.7_2.7.15~rc1-1ubuntu0.1 python2.7-minimal_2.7.15~rc1-1ubuntu0.1 readline-common_7.0-3 samtools_1.7-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10.13 systemd-sysv_237-3ubuntu10.13 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2ubuntu0.1 tzdata_2018i-0ubuntu0.18.04 ubuntu-keyring_2018.09.18.1~18.04.0 util-linux_2.31.1-0.4ubuntu3.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 6 18:21:01 2018 UTC gpgv: using RSA key 773C99EBD0A11172217A7C3FCAC2D8B9CD2CA5F9 gpgv: issuer "xnox@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.7.4+ds-1build2.dsc dpkg-source: info: extracting pbbam in pbbam-0.7.4+ds dpkg-source: info: unpacking pbbam_0.7.4+ds.orig.tar.gz dpkg-source: info: unpacking pbbam_0.7.4+ds-1build2.debian.tar.xz dpkg-source: info: applying ssl-md5.patch dpkg-source: info: applying remove-bam2sam.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16069574 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16069574 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16069574 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 0.7.4+ds-1build2 dpkg-buildpackage: info: source distribution bionic dpkg-source --before-build pbbam-0.7.4+ds dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-0.7.4+ds/gendata make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_configure -- \ -DPacBioBAM_build_shared=ON \ -DPacBioBAM_build_tests=OFF \ -DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf \ -DCMAKE_SKIP_RPATH=ON \ -DHTSLIB_INCLUDE_DIRS=/usr/include \ -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" cd obj-arm-linux-gnueabihf && cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DPacBioBAM_build_shared=ON -DPacBioBAM_build_tests=OFF -DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf -DCMAKE_SKIP_RPATH=ON -DHTSLIB_INCLUDE_DIRS=/usr/include "-DHTSLIB_LIBRARIES=-lssl -lcrypto -lhts" "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro" -- The CXX compiler identification is GNU 7.3.0 -- The C compiler identification is GNU 7.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Performing Test HAS_NO_SIGN_COMPARE -- Performing Test HAS_NO_SIGN_COMPARE - Success -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.65.1 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD - Success -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_auto_build -a cd obj-arm-linux-gnueabihf && make -j4 -O make[1]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -H/<>/pbbam-0.7.4+ds -B/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[1]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/CMakeFiles /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make[1]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/Makefile2 all make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/depend make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/src /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src/CMakeFiles/pbbam.dir/DependInfo.cmake --color= Scanning dependencies of target pbbam make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/AssertUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AssertUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/AssertUtils.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 1%] Building CXX object src/CMakeFiles/pbbam.dir/Accuracy.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Accuracy.cpp.o -c /<>/pbbam-0.7.4+ds/src/Accuracy.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o -c /<>/pbbam-0.7.4+ds/src/AlignmentPrinter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 6%] Building CXX object src/CMakeFiles/pbbam.dir/BamHeader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamHeader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamHeader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 4%] Building CXX object src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BaiIndexedBamReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 5%] Building CXX object src/CMakeFiles/pbbam.dir/BamFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamFile.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 8%] Building CXX object src/CMakeFiles/pbbam.dir/BamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 10%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordBuilder.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 11%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordImpl.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 12%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordTags.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 14%] Building CXX object src/CMakeFiles/pbbam.dir/BamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamWriter.cpp /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In member function ‘void PacBio::BAM::internal::BamWriterPrivate::Write(const PacBio::BAM::BamRecord&, int64_t*)’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:143:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzf); ~~~~~~~~~~^~~~~~ /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In destructor ‘PacBio::BAM::BamWriter::~BamWriter()’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:182:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(d_->file_.get()->fp.bgzf); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 17%] Building CXX object src/CMakeFiles/pbbam.dir/ChemistryTable.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o -c /<>/pbbam-0.7.4+ds/src/ChemistryTable.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 18%] Building CXX object src/CMakeFiles/pbbam.dir/Cigar.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Cigar.cpp.o -c /<>/pbbam-0.7.4+ds/src/Cigar.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 9%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecord.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 19%] Building CXX object src/CMakeFiles/pbbam.dir/CigarOperation.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/CigarOperation.cpp.o -c /<>/pbbam-0.7.4+ds/src/CigarOperation.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 21%] Building CXX object src/CMakeFiles/pbbam.dir/Config.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Config.cpp.o -c /<>/pbbam-0.7.4+ds/src/Config.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 13%] Building CXX object src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamTagCodec.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 22%] Building CXX object src/CMakeFiles/pbbam.dir/DataSet.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSet.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSet.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 20%] Building CXX object src/CMakeFiles/pbbam.dir/Compare.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Compare.cpp.o -c /<>/pbbam-0.7.4+ds/src/Compare.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 25%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetElement.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetElement.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetElement.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 16%] Building CXX object src/CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/BarcodeQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 26%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetIO.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 24%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetBaseTypes.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 28%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetXsd.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetXsd.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 32%] Building CXX object src/CMakeFiles/pbbam.dir/FileProducer.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileProducer.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileProducer.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 31%] Building CXX object src/CMakeFiles/pbbam.dir/FastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FastaReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 34%] Building CXX object src/CMakeFiles/pbbam.dir/FofnReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FofnReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FofnReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 33%] Building CXX object src/CMakeFiles/pbbam.dir/FileUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileUtils.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 35%] Building CXX object src/CMakeFiles/pbbam.dir/Frames.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Frames.cpp.o -c /<>/pbbam-0.7.4+ds/src/Frames.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 36%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicInterval.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicInterval.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 27%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetTypes.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 40%] Building CXX object src/CMakeFiles/pbbam.dir/IRecordWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IRecordWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/IRecordWriter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 41%] Building CXX object src/CMakeFiles/pbbam.dir/MD5.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MD5.cpp.o -c /<>/pbbam-0.7.4+ds/src/MD5.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 29%] Building CXX object src/CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/EntireFileQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 39%] Building CXX object src/CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/IndexedFastaReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 42%] Building CXX object src/CMakeFiles/pbbam.dir/MemoryUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/MemoryUtils.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 43%] Building CXX object src/CMakeFiles/pbbam.dir/PbiBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiBuilder.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 37%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicIntervalQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 44%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFile.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 47%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 48%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterTypes.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 45%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilter.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 49%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndex.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndex.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndex.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 54%] Building CXX object src/CMakeFiles/pbbam.dir/ProgramInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ProgramInfo.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 50%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexedBamReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 56%] Building CXX object src/CMakeFiles/pbbam.dir/QualityValue.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QualityValue.cpp.o -c /<>/pbbam-0.7.4+ds/src/QualityValue.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 52%] Building CXX object src/CMakeFiles/pbbam.dir/PbiRawData.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiRawData.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp In file included from /usr/include/c++/7/vector:69:0, from /<>/pbbam-0.7.4+ds/include/pbbam/PbiRawData.h:48, from /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp:42: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from /<>/pbbam-0.7.4+ds/include/pbbam/PbiRawData.h:48, from /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp:42: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiRawBasicData::AddRecord(const PacBio::BAM::BamRecord&, int64_t)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp:431:1: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 } ^ make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 51%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadHeader(PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:237:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &version, sizeof(version)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:238:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, §ions, sizeof(sections)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:239:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numReads, sizeof(numReads)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadReferenceData(PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:293:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numRefs, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:302:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.tId_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:303:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.beginRow_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:304:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.endRow_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = long long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteHeader(const PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:380:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, magic, 4); ~~~~~~~~~~^~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:391:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &version, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:392:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &pbi_flags, 2); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:393:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numReads, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:398:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, reserved, 18); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteReferenceData(const PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:434:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numRefs, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:448:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &tId, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:449:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &beginRow, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:450:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &endRow, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = long long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 55%] Building CXX object src/CMakeFiles/pbbam.dir/QNameQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QNameQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/QNameQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 58%] Building CXX object src/CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadGroupInfo.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 60%] Building CXX object src/CMakeFiles/pbbam.dir/SamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamWriter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 57%] Building CXX object src/CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadAccuracyQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 62%] Building CXX object src/CMakeFiles/pbbam.dir/SequenceInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/SequenceInfo.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 65%] Building CXX object src/CMakeFiles/pbbam.dir/TagCollection.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/TagCollection.cpp.o -c /<>/pbbam-0.7.4+ds/src/TagCollection.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 59%] Building CXX object src/CMakeFiles/pbbam.dir/SamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamTagCodec.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 67%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationErrors.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationErrors.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 68%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationException.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationException.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationException.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 63%] Building CXX object src/CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/SubreadLengthQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 64%] Building CXX object src/CMakeFiles/pbbam.dir/Tag.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Tag.cpp.o -c /<>/pbbam-0.7.4+ds/src/Tag.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 70%] Building CXX object src/CMakeFiles/pbbam.dir/Version.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Version.cpp.o -c /<>/pbbam-0.7.4+ds/src/Version.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 66%] Building CXX object src/CMakeFiles/pbbam.dir/Validator.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Validator.cpp.o -c /<>/pbbam-0.7.4+ds/src/Validator.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 74%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualRegionTypeMap.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 75%] Building CXX object src/CMakeFiles/pbbam.dir/XmlReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 71%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwBamRecord.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 73%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 72%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwCompositeReader.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 77%] Building CXX object src/CMakeFiles/pbbam.dir/XmlWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlWriter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 78%] Building CXX object src/CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/WhitelistedZmwReadStitcher.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 82%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwTypeMap.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 80%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwReadStitcher.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 79%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwGroupQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 81%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwQuery.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 83%] Building CXX object src/CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -c /<>/pbbam-0.7.4+ds/src/pugixml/pugixml.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 85%] Linking CXX shared library ../lib/libpbbam.so cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbbam.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 86%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o 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-I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/CppFormatter.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 96%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare 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directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 94%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp In file included from /usr/include/c++/7/vector:69:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/Settings.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/IFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json, std::allocator >, bool, long long int, double, std::allocator>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator {aka __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:60:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/json.hpp:52, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/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, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]’: /usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/json.hpp:52, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 4; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 10; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 12; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 11; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 5; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](const T (&)[n]) [with T = char; unsigned int n = 7; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRaw()’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/vector:69:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/Settings.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/IFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/vector.tcc: In member function ‘void pbindexdump::JsonFormatter::FormatMetadata()’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/json.hpp:52, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRecords()’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/vector:69:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/Settings.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/IFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/json.hpp:52, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatReferences()’: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/vector:69:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/Settings.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/IFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:41, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/json.hpp:52, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.h:42, from /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp:38: /usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator {aka std::_Rb_tree_const_iterator, nlohmann::basic_json<> > >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 98%] Linking CXX executable ../../bin/pbindexdump cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindexdump.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o CMakeFiles/pbindexdump.dir/src/main.cpp.o -o ../../bin/pbindexdump ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[2]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 98%] Built target pbindexdump make[2]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [ 90%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbmerge && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbmerge.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbmerge/src/main.cpp make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [100%] Linking CXX executable ../../bin/pbmerge cd /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/tools/pbmerge && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbmerge.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o CMakeFiles/pbmerge.dir/src/main.cpp.o -o ../../bin/pbmerge ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[2]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' [100%] Built target pbmerge make[2]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' make[1]: Entering directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-arm-linux-gnueabihf' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbbam-0.7.4+ds' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t mkdir -p /<>/pbbam-0.7.4+ds/gendata python tests/scripts/generate_data.py /<>/pbbam-0.7.4+ds/tests/data /<>/pbbam-0.7.4+ds/gendata Generating test data in /<>/pbbam-0.7.4+ds/gendata - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating symlink: missing_pbi.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. BINDIR=`find $PWD -name bin -type d`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: failed --- tests/src/cram/pbmerge_aligned_ordering.deb.t +++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err @@ -122,41 +122,28 @@ Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2 + pbmerge: /<>/pbbam-0.7.4+ds/src/PbiBuilder.cpp:327: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed. + Aborted (core dumped) + [134] $ samtools view -H $MERGED_BAM - @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) - @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) - @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) - @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20 - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam" for reading: No such file or directory $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found + Not found $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam': No such file or directory + [1] $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam.pbi': No such file or directory + [1] Explicit Output Filename (with disabled PBI): tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed # Ran 7 tests, 0 skipped, 1 failed. debian/rules:26: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190225-0943 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 123380 Build-Time: 286 Distribution: bionic Fail-Stage: build Host Architecture: armhf Install-Time: 36 Job: pbbam_0.7.4+ds-1build2.dsc Machine Architecture: arm64 Package: pbbam Package-Time: 325 Source-Version: 0.7.4+ds-1build2 Space: 123380 Status: attempted Version: 0.7.4+ds-1build2 -------------------------------------------------------------------------------- Finished at 20190225-0943 Build needed 00:05:25, 123380k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16069574 Scanning for processes to kill in build PACKAGEBUILD-16069574