I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 5 14:13:24 -12 2021 I: pbuilder-time-stamp: 1633486404 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pbbam_0.19.0+dfsg-4.dsc] I: copying [./pbbam_0.19.0+dfsg.orig.tar.xz] I: copying [./pbbam_0.19.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 5 20:30:46 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.19.0+dfsg-4.dsc dpkg-source: info: extracting pbbam in pbbam-0.19.0+dfsg dpkg-source: info: unpacking pbbam_0.19.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_0.19.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_gtest_depcheck.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32368/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='23d0a3b31e0c43bd9fc5c476e7f94fac' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='32368' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.CiPwizG0li/pbuilderrc_q8JT --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CiPwizG0li/b1 --logfile b1/build.log pbbam_0.19.0+dfsg-4.dsc' SUDO_GID='114' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-5 (2021-09-23) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 6 20:26 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/32368/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-exec, d-shlibs, meson, pkg-config, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python-cram, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev (>= 1.54); however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on python-cram; however: Package python-cram is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libgtest-dev{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} meson{a} mime-support{a} ninja-build{a} pkg-config{a} po-debconf{a} python{a} python-cram{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-minimal{a} python3-pkg-resources{a} python3.7{a} python3.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl cwltool krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 46.8 MB of archives. After unpacking 261 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2+deb10u1 [104 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3+deb10u1 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u6 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u3 [582 kB] Get: 23 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u3 [1466 kB] Get: 24 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u3 [1660 kB] Get: 27 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u2 [242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u2 [110 kB] Get: 33 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u2 [65.6 kB] Get: 34 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 36 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 37 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main armhf d-shlibs all 0.84 [17.2 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 43 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 48 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u3 [1102 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+deb10u2 [597 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 54 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 55 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 57 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 58 http://deb.debian.org/debian buster/main armhf dh-exec armhf 0.23.1 [24.9 kB] Get: 59 http://deb.debian.org/debian buster/main armhf googletest armhf 1.8.1-3 [903 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libboost-dev armhf 1.67.0.1 [3860 B] Get: 62 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3+deb10u1 [62.3 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3+deb10u1 [119 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3+deb10u1 [323 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3+deb10u1 [137 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u6 [202 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 73 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u2 [296 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libgtest-dev armhf 1.8.1-3 [214 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 79 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 80 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libssl-dev armhf 1.1.1d-0+deb10u6 [1598 kB] Get: 83 http://deb.debian.org/debian buster/main armhf ninja-build armhf 1.8.2-1 [83.0 kB] Get: 84 http://deb.debian.org/debian buster/main armhf python3-pkg-resources all 40.8.0-1 [153 kB] Get: 85 http://deb.debian.org/debian buster/main armhf meson all 0.49.2-1 [281 kB] Get: 86 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Get: 87 http://deb.debian.org/debian buster/main armhf python-cram all 0.7-3 [17.0 kB] Get: 88 http://deb.debian.org/debian buster/main armhf samtools armhf 1.9-4 [410 kB] Fetched 46.8 MB in 13s (3733 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u2) ... Setting up libdeflate0:armhf (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up googletest:armhf (1.8.1-3) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up ninja-build (1.8.2-1) ... Setting up libkrb5support0:armhf (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libssl-dev:armhf (1.1.1d-0+deb10u6) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up d-shlibs (0.84) ... Setting up libk5crypto3:armhf (1.17-3+deb10u1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-3+deb10u1) ... Setting up libboost-dev:armhf (1.67.0.1) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libbsd0:armhf (0.9.1-2+deb10u1) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+deb10u2) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:armhf (3.7.3-2+deb10u3) ... Setting up libgtest-dev:armhf (1.8.1-3) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3+deb10u1) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libpython3-stdlib:armhf (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up libhts2:armhf (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up meson (0.49.2-1) ... Setting up python-cram (0.7-3) ... Setting up samtools (1.9-4) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Setting up dh-exec (0.23.1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/pbbam-0.19.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbbam_0.19.0+dfsg-4_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 0.19.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbbam-0.19.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-0.19.0+dfsg/gendata make[1]: Leaving directory '/build/pbbam-0.19.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules build dh build --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson dh_auto_configure -O--buildsystem=meson cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf The Meson build system Version: 0.49.2 Source dir: /build/pbbam-0.19.0+dfsg Build dir: /build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf Build type: native build Project name: PacBioBAM Project version: 0.19.0 Appending CXXFLAGS from environment: '-g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Appending LDFLAGS from environment: '-Wl,-z,relro -Wl,-z,now' Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2' Native C++ compiler: c++ (gcc 8.3.0 "c++ (Debian 8.3.0-6) 8.3.0") Build machine cpu family: arm Build machine cpu: arm Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Dependency threads found: YES Dependency Boost found: YES 1.67 Found pkg-config: /usr/bin/pkg-config (0.29) Dependency zlib found: YES 1.2.11 Dependency htslib found: YES 1.9 Program python found: YES (/usr/bin/python) Program tools/check-formatting found: YES (/build/pbbam-0.19.0+dfsg/tools/check-formatting) Program cram found: YES (/usr/bin/cram) Dependency GTest found: YES (prebuilt) Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Build targets in project: 8 Option buildtype is: plain [default: release] Found ninja-1.8.2 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j3 -v [1/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -MF 'src/25a6634@@pbbam@sha/Accuracy.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -c ../src/Accuracy.cpp [2/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -c ../src/BaiIndexedBamReader.cpp [3/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -MF 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -c ../src/AlignmentPrinter.cpp [4/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -c ../src/BamFile.cpp [5/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -c ../src/BamReader.cpp [6/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamHeader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -c ../src/BamHeader.cpp [7/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -c ../src/BamRecordBuilder.cpp [8/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecord.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' -c ../src/BamRecord.cpp [9/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' -c ../src/BamRecordTags.cpp [10/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -c ../src/BamRecordImpl.cpp [11/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' -c ../src/BamWriter.cpp [12/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' -MF 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' -c ../src/ChemistryTable.cpp [13/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Cigar.cpp.o' -MF 'src/25a6634@@pbbam@sha/Cigar.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Cigar.cpp.o' -c ../src/Cigar.cpp [14/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' -MF 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o.d' -o 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' -c ../src/CigarOperation.cpp [15/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' -c ../src/BamTagCodec.cpp [16/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Config.cpp.o' -MF 'src/25a6634@@pbbam@sha/Config.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Config.cpp.o' -c ../src/Config.cpp [17/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' -c ../src/BarcodeQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/BarcodeQuery.cpp:13: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [18/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSet.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSet.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSet.cpp.o' -c ../src/DataSet.cpp [19/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Compare.cpp.o' -MF 'src/25a6634@@pbbam@sha/Compare.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Compare.cpp.o' -c ../src/Compare.cpp [20/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' -c ../src/DataSetElement.cpp [21/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' -c ../src/DataSetBaseTypes.cpp [22/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' -c ../src/DataSetXsd.cpp [23/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' -c ../src/DataSetIO.cpp [24/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' -c ../src/DataSetTypes.cpp [25/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' -c ../src/FastaReader.cpp [26/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastqReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' -c ../src/FastqReader.cpp [27/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' -MF 'src/25a6634@@pbbam@sha/FileProducer.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' -c ../src/FileProducer.cpp [28/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' -c ../src/EntireFileQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/EntireFileQuery.cpp:11: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [29/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FofnReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' -c ../src/FofnReader.cpp [30/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Frames.cpp.o' -MF 'src/25a6634@@pbbam@sha/Frames.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Frames.cpp.o' -c ../src/Frames.cpp [31/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' -c ../src/FastaSequenceQuery.cpp [32/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' -MF 'src/25a6634@@pbbam@sha/FileUtils.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' -c ../src/FileUtils.cpp [33/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' -MF 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o.d' -o 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' -c ../src/GenomicInterval.cpp [34/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' -c ../src/IndexedBamWriter.cpp [35/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' -c ../src/GenomicIntervalQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/GenomicIntervalQuery.cpp:11: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [36/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/MD5.cpp.o' -MF 'src/25a6634@@pbbam@sha/MD5.cpp.o.d' -o 'src/25a6634@@pbbam@sha/MD5.cpp.o' -c ../src/MD5.cpp [37/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' -c ../src/IndexedFastaReader.cpp [38/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' -MF 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o.d' -o 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' -c ../src/MemoryUtils.cpp [39/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' -c ../src/PbiBuilder.cpp In file included from /usr/include/c++/8/vector:69, from ../include/pbbam/BamHeader.h:15, from ../src/MemoryUtils.h:12, from ../src/PbiBuilder.cpp:26: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/pbbam/BamHeader.h:15, from ../src/MemoryUtils.h:12, from ../src/PbiBuilder.cpp:26: /usr/include/c++/8/bits/stl_vector.h: In member function ‘void PacBio::BAM::internal::PbiBuilderPrivate::AddBasicData(const PacBio::BAM::BamRecord&, int64_t)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [40/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' -c ../src/PbiFile.cpp [41/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' -c ../src/PbiFilterQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiFilterQuery.h:12, from ../src/PbiFilterQuery.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [42/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' -c ../src/PbiFilter.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../src/PbiFilter.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [43/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' -c ../src/PbiFilterTypes.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../src/PbiFilterTypes.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [44/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' -c ../src/PbiIndexedBamReader.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../src/PbiIndexedBamReader.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [45/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' -c ../src/PbiRawData.cpp In file included from /usr/include/c++/8/vector:69, from ../include/pbbam/PbiRawData.h:13, from ../src/PbiRawData.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../include/pbbam/PbiRawData.h:13, from ../src/PbiRawData.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiRawBasicData::AddRecord(const PacBio::BAM::BamRecord&, int64_t)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [46/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' -c ../src/PbiIndexIO.cpp [47/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' -c ../src/ProgramInfo.cpp [48/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' -MF 'src/25a6634@@pbbam@sha/QualityValue.cpp.o.d' -o 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' -c ../src/QualityValue.cpp [49/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' -c ../src/QNameQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/QNameQuery.cpp:15: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [50/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c ../tests/src/test_BamRecordClipping.cpp [51/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' -c ../src/ReadAccuracyQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/ReadAccuracyQuery.cpp:11: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [52/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' -c ../src/ReadGroupInfo.cpp [53/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/SamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' -c ../src/SamWriter.cpp [54/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' -MF 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' -c ../src/SamTagCodec.cpp [55/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' -c ../src/SequenceInfo.cpp [56/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' -MF 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' -c ../src/ValidationErrors.cpp [57/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' -c ../src/SubreadLengthQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/SubreadLengthQuery.cpp:13: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [58/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' -MF 'src/25a6634@@pbbam@sha/ValidationException.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' -c ../src/ValidationException.cpp [59/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Validator.cpp.o' -MF 'src/25a6634@@pbbam@sha/Validator.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Validator.cpp.o' -c ../src/Validator.cpp [60/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Version.cpp.o' -MF 'src/25a6634@@pbbam@sha/Version.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Version.cpp.o' -c ../src/Version.cpp [61/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' -c ../src/VirtualZmwBamRecord.cpp [62/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' -c ../src/VirtualRegionTypeMap.cpp [63/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' -c ../src/VirtualZmwCompositeReader.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../src/VirtualZmwReader.h:16, from ../src/VirtualZmwCompositeReader.h:15, from ../src/VirtualZmwCompositeReader.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [64/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' -c ../src/XmlWriter.cpp [65/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' -c ../src/VirtualZmwReader.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../src/VirtualZmwReader.h:16, from ../src/VirtualZmwReader.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [66/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/XmlReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' -c ../src/XmlReader.cpp [67/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' -MF 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o.d' -o 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' -c ../src/WhitelistedZmwReadStitcher.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../src/VirtualZmwReader.h:16, from ../src/WhitelistedZmwReadStitcher.cpp:14: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [68/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' -c ../src/ZmwReadStitcher.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../src/VirtualZmwReader.h:16, from ../src/ZmwReadStitcher.cpp:15: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [69/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' -c ../src/ZmwTypeMap.cpp [70/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' -c ../src/vcf/VcfVariant.cpp [71/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' -c ../src/ZmwGroupQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/ZmwGroupQuery.cpp:17: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [72/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' -c ../src/vcf/VcfHeader.cpp [73/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' -c ../src/vcf/VcfReader.cpp [74/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' -c ../src/vcf/VcfFormat.cpp [75/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' -c ../src/ZmwQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiIndexedBamReader.h:14, from ../include/pbbam/CompositeBamReader.h:24, from ../src/ZmwQuery.cpp:13: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [76/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' -c ../src/vcf/VcfWriter.cpp [77/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' -c ../src/vcf/VcfQuery.cpp [78/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -MF 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o.d' -o 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -c ../src/pugixml/pugixml.cpp [79/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' -c ../src/vcf/VcfSort.cpp [80/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -c ../tests/src/test_BamRecordBuilder.cpp [81/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -c ../tests/src/test_AlignmentPrinter.cpp [82/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' -c ../tests/src/test_Accuracy.cpp [83/161] c++ -o src/libpbbam.so.0.19.0 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamFile.cpp.o' 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' 'src/25a6634@@pbbam@sha/BamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' 'src/25a6634@@pbbam@sha/Cigar.cpp.o' 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' 'src/25a6634@@pbbam@sha/Compare.cpp.o' 'src/25a6634@@pbbam@sha/Config.cpp.o' 'src/25a6634@@pbbam@sha/DataSet.cpp.o' 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' 'src/25a6634@@pbbam@sha/Frames.cpp.o' 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/MD5.cpp.o' 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' 'src/25a6634@@pbbam@sha/Validator.cpp.o' 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' 'src/25a6634@@pbbam@sha/Version.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -Wl,--no-undefined -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.0.19.0 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhts.so -Wl,--end-group -pthread [84/161] /usr/bin/meson --internal symbolextractor src/libpbbam.so.0.19.0 'src/25a6634@@pbbam@sha/libpbbam.so.0.19.0.symbols' [85/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -c ../tests/src/test_BamFile.cpp [86/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' -c ../tests/src/test_BamHeader.cpp [87/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -c ../tests/src/test_BamRecordImplCore.cpp [88/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' -c ../tests/src/test_BamRecord.cpp [89/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -c ../tests/src/test_BamRecordImplTags.cpp [90/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c ../tests/src/test_BamWriter.cpp [91/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -c ../tests/src/test_BarcodeQuery.cpp [92/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -c ../tests/src/test_Cigar.cpp [93/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c ../tests/src/test_BamRecordMapping.cpp [94/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -c ../tests/src/test_DataSetCore.cpp [95/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -c ../tests/src/test_Compare.cpp [96/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' -c ../tests/src/test_DataSetIO.cpp [97/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -c ../tests/src/test_BamRecordImplVariableData.cpp [98/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' -c ../tests/src/test_DataSetXsd.cpp [99/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -c ../tests/src/test_DataSetQuery.cpp [100/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' -c ../tests/src/test_EndToEnd.cpp [101/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' -c ../tests/src/test_Fastq.cpp [102/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -c ../tests/src/test_EntireFileQuery.cpp [103/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -c ../tests/src/test_Fasta.cpp [104/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -c ../tests/src/test_Frames.cpp [105/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' -c ../tests/src/test_FileUtils.cpp [106/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -c ../tests/src/test_IndexedBamWriter.cpp [107/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' -c ../tests/src/test_GenomicIntervalQuery.cpp [108/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -c ../tests/src/test_IndexedFastaReader.cpp [109/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -c ../tests/src/test_Intervals.cpp [110/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -c ../tests/src/test_LongCigar.cpp [111/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -c ../tests/src/test_PacBioIndex.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/gtest/gtest.h:57, from ../tests/src/test_PacBioIndex.cpp:8: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/gtest/gtest.h:57, from ../tests/src/test_PacBioIndex.cpp:8: /usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual void PacBioIndexTest_CreateOnTheFly_Test::TestBody()’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [112/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -c ../tests/src/test_QNameQuery.cpp [113/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -c ../tests/src/test_PbiFilterQuery.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../include/pbbam/PbiFilterQuery.h:12, from ../tests/src/test_PbiFilterQuery.cpp:14: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [114/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -c ../tests/src/test_QualityValues.cpp [115/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -c ../tests/src/test_Pulse2BaseCache.cpp [116/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -c ../tests/src/test_ReadAccuracyQuery.cpp [117/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -c ../tests/src/test_ReadGroupInfo.cpp [118/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -c ../tests/src/test_PbiFilter.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../tests/src/test_PbiFilter.cpp:14: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [119/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -c ../tests/src/test_StringUtils.cpp [120/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -c ../tests/src/test_SequenceUtils.cpp [121/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -c ../tests/src/test_SamWriter.cpp [122/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -c ../tests/src/test_TimeUtils.cpp [123/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -c ../tests/src/test_SubreadLengthQuery.cpp [124/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -c ../tests/src/test_VcfFile.cpp [125/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -c ../tests/src/test_VcfFormat.cpp [126/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -c ../tests/src/test_Validator.cpp [127/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -c ../tests/src/test_VcfReader.cpp [128/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -c ../tests/src/test_VcfHeader.cpp [129/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -c ../tests/src/test_Tags.cpp [130/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -c ../tests/src/test_VcfSort.cpp [131/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -c ../tests/src/test_VcfQuery.cpp [132/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -c ../tests/src/test_VcfVariant.cpp [133/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -c ../tests/src/test_Version.cpp [134/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -c ../tests/src/test_VcfWriter.cpp [135/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -c ../tests/src/test_ZmwQuery.cpp [136/161] /usr/bin/python ../tests/scripts/generate_data.py /build/pbbam-0.19.0+dfsg/tests/data /build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/tests Generating test data in /build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/tests - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fq...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. [137/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [138/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -c ../tools/pbindex/src/PbIndex.cpp [139/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [140/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [141/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -c ../tools/bam2sam/src/Bam2Sam.cpp [142/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -c ../tests/src/test_ZmwReadStitcher.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../tests/src/test_ZmwReadStitcher.cpp:11: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [143/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -c ../tools/pbindex/src/main.cpp [144/161] c++ -o tools/pbindex 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/src [145/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -c ../tools/bam2sam/src/main.cpp [146/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -c ../tools/pbindexdump/src/CppFormatter.cpp [147/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [148/161] c++ -o tools/bam2sam 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group -pthread [149/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -c ../tools/pbindexdump/src/PbIndexDump.cpp [150/161] c++ -o tests/pbbam_test 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 -lgtest -lgtest_main /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/src [151/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -c ../tools/pbindexdump/src/main.cpp [152/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -c ../tools/pbindexdump/src/JsonFormatter.cpp In file included from /usr/include/c++/8/vector:69, from ../include/pbbam/PbiRawData.h:13, from ../tools/pbindexdump/src/JsonFormatter.h:6, from ../tools/pbindexdump/src/JsonFormatter.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json, std::allocator >, bool, long long int, double, std::allocator>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../tools/pbindexdump/src/json.hpp:54, from ../tools/pbindexdump/src/JsonFormatter.h:8, from ../tools/pbindexdump/src/JsonFormatter.cpp:3: /usr/include/c++/8/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]’: /usr/include/c++/8/bits/stl_tree.h:2411:7: 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++/8/map:61, from ../tools/pbindexdump/src/json.hpp:54, from ../tools/pbindexdump/src/JsonFormatter.h:8, from ../tools/pbindexdump/src/JsonFormatter.cpp:3: /usr/include/c++/8/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++/8/bits/stl_map.h:518:8: 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++/8/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++/8/bits/stl_map.h:518:8: 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++/8/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++/8/bits/stl_map.h:518:8: 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++/8/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++/8/bits/stl_map.h:518:8: 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++/8/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++/8/bits/stl_map.h:518:8: 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++/8/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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRaw()’: /usr/include/c++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatMetadata()’: /usr/include/c++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRecords()’: /usr/include/c++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatReferences()’: /usr/include/c++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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++/8/bits/stl_map.h:518:8: 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, [153/161] c++ -o tools/pbindexdump 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/src [154/161] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [155/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [156/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -c ../tools/pbbamify/src/main.cpp [157/161] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -c ../tools/pbmerge/src/main.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../tools/pbmerge/../common/BamFileMerger.h:7, from ../tools/pbmerge/src/main.cpp:9: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [158/161] c++ -o tools/pbmerge 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/src [159/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -c ../tools/pbbamify/src/PbBamify.cpp In file included from ../include/pbbam/PbiFilterTypes.h:897, from ../include/pbbam/PbiFilter.h:244, from ../tools/pbbamify/src/PbBamify.cpp:8: ../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’: ../include/pbbam/internal/PbiFilterTypes.inl:472:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast] return static_cast(seed); ^ [160/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -c ../tools/pbbamify/src/QueryLookup.cpp [161/161] c++ -o tools/pbbamify 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-0.19.0+dfsg/obj-arm-linux-gnueabihf/src debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-0.19.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/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@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/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@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/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@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.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@|/build/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t dh_auto_configure -O--buildsystem=meson cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. If ninja fails, run "ninja reconfigure" or "meson --reconfigure" to force Meson to regenerate. If build failures persist, run "meson setup --wipe" to rebuild from scratch using the same options as passed when configuring the build. To change option values, run "meson configure" instead. mkdir -p /build/pbbam-0.19.0+dfsg/gendata python tests/scripts/generate_data.py /build/pbbam-0.19.0+dfsg/tests/data /build/pbbam-0.19.0+dfsg/gendata Generating test data in /build/pbbam-0.19.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fq...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. # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v --preserve-env 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/pbbamify.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 @@ -122,6 +122,8 @@ Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2 + ERROR: stoul + [1] $ samtools view -H $MERGED_BAM @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) @@ -132,25 +134,6 @@ $ 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) $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Found 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/pbbamify.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed # Ran 8 tests, 0 skipped, 1 failed. make[1]: *** [debian/rules:22: override_dh_auto_test] Error 1 make[1]: Leaving directory '/build/pbbam-0.19.0+dfsg' make: *** [debian/rules:13: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/32368 and its subdirectories