I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 16 05:40:48 -12 2021 I: pbuilder-time-stamp: 1631814048 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 [pbseqlib_5.3.1+dfsg-2.1.dsc] I: copying [./pbseqlib_5.3.1+dfsg.orig.tar.xz] I: copying [./pbseqlib_5.3.1+dfsg-2.1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 5 19:10:41 2019 -12 gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.1+dfsg-2.1.dsc dpkg-source: info: extracting pbseqlib in pbseqlib-5.3.1+dfsg dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg-2.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hdf5-1.10.1-support.patch dpkg-source: info: applying hdf5-1.10.0-support.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27219/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='27219' 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.rRZxK5wi5G/pbuilderrc_Hxv4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.rRZxK5wi5G/b1 --logfile b1/build.log pbseqlib_5.3.1+dfsg-2.1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled11-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 15 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 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/27219/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: arm64 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, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libhts-dev, libgtest-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbbam-dev (>= 0.18.0+dfsg-1~); however: Package libpbbam-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. 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} 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} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{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} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libgtest-dev{a} libhdf5-103{a} libhdf5-cpp-103{a} libhdf5-dev{a} libhts-dev{a} libhts2{a} libicu63{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{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} libncurses6{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam0.19.0{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl 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, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 47.8 MB of archives. After unpacking 276 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 dh-exec arm64 0.23.1 [25.9 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 googletest arm64 1.8.1-3 [903 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 hdf5-helpers arm64 1.10.4+repack-10 [35.2 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libaec0 arm64 1.0.2-1 [18.8 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libsz2 arm64 1.0.2-1 [6456 B] Get: 54 http://deb.debian.org/debian buster/main arm64 libaec-dev arm64 1.0.2-1 [17.1 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libboost-dev arm64 1.67.0.1 [3864 B] Get: 57 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libcurl3-gnutls arm64 7.64.0-4+deb10u1 [310 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libgtest-dev arm64 1.8.1-3 [218 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 libhdf5-103 arm64 1.10.4+repack-10 [1168 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libhdf5-cpp-103 arm64 1.10.4+repack-10 [132 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo arm64 1:1.5.2-2+b1 [115 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo-dev arm64 1:1.5.2-2+b1 [186 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 libjpeg-dev all 1:1.5.2-2 [57.5 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 libhdf5-dev arm64 1.10.4+repack-10 [2683 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 libhts2 arm64 1.9-11 [277 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 liblzma-dev arm64 5.2.4-1 [209 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libhts-dev arm64 1.9-11 [4338 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libpbbam0.19.0 arm64 0.19.0+dfsg-4 [492 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 libssl-dev arm64 1.1.1d-0+deb10u3 [1685 kB] Get: 86 http://deb.debian.org/debian buster/main arm64 libpbbam-dev arm64 0.19.0+dfsg-4 [93.3 kB] Fetched 47.8 MB in 4s (11.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Setting up libkeyutils1:arm64 (1.6-6) ... Setting up libpsl5:arm64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up hdf5-helpers (1.10.4+repack-10) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up libdeflate0:arm64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up googletest:arm64 (1.8.1-3) ... Setting up libaec0:arm64 (1.0.2-1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libkrb5support0:arm64 (1.17-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:arm64 (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:arm64 (1:1.5.2-2+b1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libssl-dev:arm64 (1.1.1d-0+deb10u3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:arm64 (8.3.0-6) ... Setting up liblzma-dev:arm64 (5.2.4-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up libboost-dev:arm64 (1.67.0.1) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libsz2:arm64 (1.0.2-1) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgtest-dev:arm64 (1.8.1-3) ... Setting up libtool (2.4.6-9) ... Setting up libaec-dev:arm64 (1.0.2-1) ... Setting up libjpeg-dev (1:1.5.2-2) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up libhdf5-103:arm64 (1.10.4+repack-10) ... 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:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up libhdf5-cpp-103:arm64 (1.10.4+repack-10) ... Setting up libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... 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:arm64 (2.7.16-1) ... Setting up libhdf5-dev (1.10.4+repack-10) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python (2.7.16-1) ... Setting up libhts2:arm64 (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:arm64 (1.9-11) ... Setting up libpbbam0.19.0:arm64 (0.19.0+dfsg-4) ... Setting up libpbbam-dev (0.19.0+dfsg-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-exec (0.23.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... 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/pbseqlib-5.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.1+dfsg-2.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Adrian Bunk dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg' dh_auto_clean make -j8 clean make[2]: Entering directory '/build/pbseqlib-5.3.1+dfsg' make -C /build/pbseqlib-5.3.1+dfsg//pbdata clean make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/pbdata' rm -f libpbdata.a libpbdata.so *.o *.d make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/pbdata' make -C /build/pbseqlib-5.3.1+dfsg//hdf clean make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/hdf' rm -f libpbihdf.a libpbihdf.so *.o *.d make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/hdf' make -C /build/pbseqlib-5.3.1+dfsg//alignment clean make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/alignment' rm -f libblasr.a libblasr.so *.o *.d make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/alignment' make -C /build/pbseqlib-5.3.1+dfsg//unittest clean make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/unittest' rm -f -r *.o libblasr-test-runner make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/unittest' make[2]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' find -name defines.mk -delete rm -f pbdata/libconfig.h make[1]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg' ./configure.py PREFIX=/usr/ uname -s uname='Linux' writing to '/build/pbseqlib-5.3.1+dfsg/pbdata/LibBlasrConfig.h' """ #define USE_PBBAM """ writing to 'defines.mk' """ CXXFLAGS := -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 PREFIX_INC := /usr/include PREFIX_LIB := /usr/lib SH_LIB_EXT := .so GTEST_INC ?= /usr/include GTEST_SRCDIR ?= /usr/src/gtest HDF5_INC ?= /usr/include/hdf5/serial HDF5_LIB ?= /usr/lib/aarch64-linux-gnu/hdf5/serial LIBBLASR_INC ?= ../alignment LIBBLASR_LIB ?= ../alignment/ LIBPBDATA_INC ?= ../pbdata LIBPBDATA_LIB ?= ../pbdata/ LIBPBIHDF_INC ?= ../hdf LIBPBIHDF_LIB ?= ../hdf/ SHELL ?= bash # Use PREFIX dir, if available. INCLUDES += ${PREFIX_INC} ../pbdata LIBS += ${PREFIX_LIB} """ make[1]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg' dh_auto_build -- PREFIX_INC=.. make -j8 "INSTALL=install --strip-program=true" PREFIX_INC=.. make[2]: Entering directory '/build/pbseqlib-5.3.1+dfsg' make libpbdata make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg' make -C /build/pbseqlib-5.3.1+dfsg//pbdata LibBlasrConfig.h make[4]: Entering directory '/build/pbseqlib-5.3.1+dfsg/pbdata' make[4]: 'LibBlasrConfig.h' is up to date. make[4]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/pbdata' make -C /build/pbseqlib-5.3.1+dfsg//pbdata all make[4]: Entering directory '/build/pbseqlib-5.3.1+dfsg/pbdata' g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/TimeUtils.cpp -o TimeUtils.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTTitle.cpp -o SMRTTitle.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/BitUtils.cpp -o BitUtils.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMHeader.cpp -o SAMHeader.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMAlignment.cpp -o SAMAlignment.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReferenceSequence.cpp -o ReferenceSequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReadGroup.cpp -o ReadGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefInfo.cpp -o RefInfo.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefGroup.cpp -o RefGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/MovieInfo.cpp -o MovieInfo.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/AlnGroup.cpp -o AlnGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ScanData.cpp -o ScanData.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTypeMap.cpp -o RegionTypeMap.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTable.cpp -o RegionTable.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotations.cpp -o RegionAnnotations.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotation.cpp -o RegionAnnotation.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ReadType.cpp -o ReadType.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseFile.cpp -o PulseFile.o In file included from reads/RegionAnnotations.cpp:3: reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const': ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ ^~~ reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW' BLASR_THROW("Zmw has more than one HQRegion"); ^~~~~~~~~~~ reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause else ^~~~ g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/HoleXY.cpp -o HoleXY.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/BaseFile.cpp -o BaseFile.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/AcqParams.cpp -o AcqParams.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/QualityTransform.cpp -o QualityTransform.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c metagenome/TitleTable.cpp -o TitleTable.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MetricField.cpp -o MetricField.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c amos/AfgBasWriter.cpp -o AfgBasWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c alignment/CmpAlignment.cpp -o CmpAlignment.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c StringUtils.cpp -o StringUtils.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c SMRTSequence.cpp -o SMRTSequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c PackedDNASequence.cpp -o PackedDNASequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c NucConversion.cpp -o NucConversion.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c MD5Utils.cpp -o MD5Utils.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c GFFFile.cpp -o GFFFile.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTQSequence.cpp -o FASTQSequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTASequence.cpp -o FASTASequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c DNASequence.cpp -o DNASequence.o In file included from SMRTSequence.cpp:3: SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const': ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ ^~~ SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW' BLASR_THROW("Base must be in A, C, G, T"); ^~~~~~~~~~~ SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause else ^~~~ g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CommandLineParser.cpp -o CommandLineParser.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ChangeListID.cpp -o ChangeListID.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CCSSequence.cpp -o CCSSequence.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTQReader.cpp -o BlasrFASTQReader.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTAReader.cpp -o BlasrFASTAReader.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ScanData.cpp -o ScanData.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o In file included from reads/RegionAnnotations.cpp:3: reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const': ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ ^~~ reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW' BLASR_THROW("Zmw has more than one HQRegion"); ^~~~~~~~~~~ reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause else ^~~~ g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ReadType.cpp -o ReadType.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c StringUtils.cpp -o StringUtils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c NucConversion.cpp -o NucConversion.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c GFFFile.cpp -o GFFFile.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c DNASequence.cpp -o DNASequence.shared.o In file included from SMRTSequence.cpp:3: SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const': ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ ^~~ SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW' BLASR_THROW("Base must be in A, C, G, T"); ^~~~~~~~~~~ SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause else ^~~~ g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTQReader.cpp -o BlasrFASTQReader.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTAReader.cpp -o BlasrFASTAReader.shared.o ar rc libpbdata.a TimeUtils.o SMRTTitle.o SMRTReadUtils.o BitUtils.o SAMKeywordValuePair.o SAMHeader.o SAMAlignment.o ReferenceSequence.o ReadGroup.o RefInfo.o RefGroup.o MovieInfo.o AlnGroup.o ZMWGroupEntry.o ScanData.o RegionTypeMap.o RegionTable.o RegionAnnotations.o RegionAnnotation.o ReadType.o PulseFile.o PulseBaseCommon.o HoleXY.o BaseFile.o AcqParams.o QualityTransform.o BlasrQualityValue.o TitleTable.o MovieAlnIndexLookupTable.o MetricField.o AfgBasWriter.o CmpAlignment.o StringUtils.o SMRTSequence.o ReverseCompressIndex.o PackedDNASequence.o NucConversion.o MD5Utils.o GFFFile.o FASTQSequence.o FASTASequence.o DNASequence.o CommandLineParser.o ChangeListID.o CCSSequence.o BlasrFASTQReader.o BlasrFASTAReader.o g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -o libpbdata.so -Wl,-soname,libpbdata.so TimeUtils.shared.o SMRTTitle.shared.o SMRTReadUtils.shared.o BitUtils.shared.o SAMKeywordValuePair.shared.o SAMHeader.shared.o SAMAlignment.shared.o ReferenceSequence.shared.o ReadGroup.shared.o RefInfo.shared.o RefGroup.shared.o MovieInfo.shared.o AlnGroup.shared.o ZMWGroupEntry.shared.o ScanData.shared.o RegionTypeMap.shared.o RegionTable.shared.o RegionAnnotations.shared.o RegionAnnotation.shared.o ReadType.shared.o PulseFile.shared.o PulseBaseCommon.shared.o HoleXY.shared.o BaseFile.shared.o AcqParams.shared.o QualityTransform.shared.o BlasrQualityValue.shared.o TitleTable.shared.o MovieAlnIndexLookupTable.shared.o MetricField.shared.o AfgBasWriter.shared.o CmpAlignment.shared.o StringUtils.shared.o SMRTSequence.shared.o ReverseCompressIndex.shared.o PackedDNASequence.shared.o NucConversion.shared.o MD5Utils.shared.o GFFFile.shared.o FASTQSequence.shared.o FASTASequence.shared.o DNASequence.shared.o CommandLineParser.shared.o ChangeListID.shared.o CCSSequence.shared.o BlasrFASTQReader.shared.o BlasrFASTAReader.shared.o -lpbbam -lpbbam make[4]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/pbdata' make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' make libpbihdf make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg' make -C /build/pbseqlib-5.3.1+dfsg//hdf all make[4]: Entering directory '/build/pbseqlib-5.3.1+dfsg/hdf' g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionsWriter.cpp -o HDFRegionsWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataReader.cpp -o HDFScanDataReader.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFData.cpp -o HDFData.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFFile.cpp -o HDFFile.o HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)': HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ HDFFile.cpp: In member function 'void HDFFile::Open(std::__cxx11::string, unsigned int, const H5::FileAccPropList&)': HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=] } catch (FileIException e) { ^ HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=] } catch (FileIException fileException) { ^~~~~~~~~~~~~ g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.o In file included from HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^~~~~ ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = char; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = long unsigned int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = float; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector >; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWMetricsWriter.hpp:7, from HDFZMWMetricsWriter.cpp:3: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]': HDFZMWMetricsWriter.cpp:54:27: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFZMWMetricsWriter.cpp:55:30: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFCmpExperimentGroup.hpp:10, from HDFCmpExperimentGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = unsigned char]' HDFCmpExperimentGroup.cpp:36:69: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = char]' HDFCmpExperimentGroup.cpp:199:72: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()': HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFPulseCallsWriter.hpp:12, from HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:492:47: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:497:39: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:498:49: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()': HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:12, from HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFBaseCallsWriter.cpp:342:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]': HDFBaseCallsWriter.cpp:350:35: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWWriter.hpp:11, from HDFZMWWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': HDFZMWWriter.cpp:149:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFZMWWriter.cpp:151:28: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseWriter.cpp -o HDFPulseWriter.o In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFAlnGroupGroup.hpp:6, from HDFAlnGroupGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]' HDFAlnGroupGroup.cpp:16:29: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = unsigned int]' HDFAlnGroupGroup.cpp:18:25: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)': HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFData.cpp -o HDFData.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFFile.cpp -o HDFFile.shared.o HDFFile.cpp: In member function 'void HDFFile::Open(std::__cxx11::string, unsigned int, const H5::FileAccPropList&)': HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=] } catch (FileIException e) { ^ HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=] } catch (FileIException fileException) { ^~~~~~~~~~~~~ g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o In file included from HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^~~~~ ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = char; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = long unsigned int; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = float; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] ../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector >; std::__cxx11::string = std::__cxx11::basic_string]': HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWMetricsWriter.hpp:7, from HDFZMWMetricsWriter.cpp:3: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]': HDFZMWMetricsWriter.cpp:54:27: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFZMWMetricsWriter.cpp:55:30: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFCmpExperimentGroup.hpp:10, from HDFCmpExperimentGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = unsigned char]' HDFCmpExperimentGroup.cpp:36:69: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = char]' HDFCmpExperimentGroup.cpp:199:72: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()': HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()': HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=] } catch (H5::Exception e) { ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFPulseCallsWriter.hpp:12, from HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:492:47: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:497:39: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': HDFPulseCallsWriter.cpp:498:49: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:12, from HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFBaseCallsWriter.cpp:342:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]': HDFBaseCallsWriter.cpp:350:35: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWWriter.hpp:11, from HDFZMWWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': HDFZMWWriter.cpp:149:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]': HDFZMWWriter.cpp:151:28: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.o g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o ar rc libpbihdf.a HDFAttributable.o BufferedHDFArray.o HDFRegionsWriter.o HDFScanDataReader.o HDFWriterBase.o HDFData.o DatasetCollection.o HDFFile.o HDFRegionTableReader.o HDFZMWMetricsWriter.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFBaseCallsWriter.o HDFCmpSupportedFields.o HDFZMWReader.o HDFZMWWriter.o HDFAlnInfoGroup.o HDFNewBasReader.o HDFAlnGroupGroup.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFScanDataWriter.o HDFBaxWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFAlnGroupGroup.hpp:6, from HDFAlnGroupGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]' HDFAlnGroupGroup.cpp:16:29: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]': ../hdf/HDFArray.hpp:67:9: required from 'void HDFArray::Write(const T*, int) [with T = unsigned int]' HDFAlnGroupGroup.cpp:18:25: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o BufferedHDFArray.shared.o HDFRegionsWriter.shared.o HDFScanDataReader.shared.o HDFWriterBase.shared.o HDFData.shared.o DatasetCollection.shared.o HDFFile.shared.o HDFRegionTableReader.shared.o HDFZMWMetricsWriter.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFBaseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFZMWReader.shared.o HDFZMWWriter.shared.o HDFAlnInfoGroup.shared.o HDFNewBasReader.shared.o HDFAlnGroupGroup.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFScanDataWriter.shared.o HDFBaxWriter.shared.o HDFPulseH5Writer.shared.o BufferedHDF2DArray.shared.o -lpbbam -lpbbam -lpbdata -lhdf5 -lhdf5_cpp make[4]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/hdf' make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' make libblasr make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg' make -C /build/pbseqlib-5.3.1+dfsg//alignment all make[4]: Entering directory '/build/pbseqlib-5.3.1+dfsg/alignment' g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/RegionUtils.cpp -o RegionUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/RangeUtils.cpp -o RangeUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/PhredUtils.cpp -o PhredUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/LogUtils.cpp -o LogUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/FileOfFileNames.cpp -o FileOfFileNames.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/BlasrFileUtils.cpp -o BlasrFileUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/TupleMetrics.cpp -o TupleMetrics.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/DNATuple.cpp -o DNATuple.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/BaseTuple.cpp -o BaseTuple.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/pdfs.cpp -o pdfs.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/cdfs.cpp -o cdfs.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/StatUtils.cpp -o StatUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/QualitySample.cpp -o QualitySample.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/LengthHistogram.cpp -o LengthHistogram.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/ContextSet.cpp -o ContextSet.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/ContextSample.cpp -o ContextSample.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c qvs/QualityValueProfile.cpp -o QualityValueProfile.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SummaryPrinter.cpp -o SummaryPrinter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SAMPrinter.cpp -o SAMPrinter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/IntervalPrinter.cpp -o IntervalPrinter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool, bool)': files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] } catch (std::exception e) { ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:8, from files/ReaderAgglomerate.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:360:50: required from here ../hdf/HDFBasReader.hpp:602:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:401:50: required from here ../hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:516:50: required from here ../hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:611:64: required from here ../hdf/HDFBasReader.hpp:691:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ In file included from ../alignment/files/ReaderAgglomerate.hpp:9, from files/ReaderAgglomerate.cpp:1: ../hdf/HDFCCSReader.hpp: In instantiation of 'int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]': files/ReaderAgglomerate.cpp:664:50: required from here ../hdf/HDFCCSReader.hpp:270:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/CCSIterator.cpp -o CCSIterator.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/BaseSequenceIO.cpp -o BaseSequenceIO.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/MatchPos.cpp -o MatchPos.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/ClusterList.cpp -o ClusterList.o files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)': files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=] std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl; ^~~~ files/ReaderAgglomerate.cpp:626:9: note: here case FileType::Fourbit: ^~~~ files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)': files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=] std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl; ^~~~ files/ReaderAgglomerate.cpp:671:9: note: here case FileType::Fourbit: ^~~~ g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/CmpFile.cpp -o CmpFile.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/Alignment.cpp -o Alignment.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/qsufsort.cpp -o qsufsort.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/Coordinate.cpp -o Coordinate.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c MappingMetrics.cpp -o MappingMetrics.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/RegionUtils.cpp -o RegionUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/RangeUtils.cpp -o RangeUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/PhredUtils.cpp -o PhredUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/LogUtils.cpp -o LogUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/FileOfFileNames.cpp -o FileOfFileNames.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/BlasrFileUtils.cpp -o BlasrFileUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/TupleMetrics.cpp -o TupleMetrics.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/DNATuple.cpp -o DNATuple.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/BaseTuple.cpp -o BaseTuple.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/pdfs.cpp -o pdfs.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/cdfs.cpp -o cdfs.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/StatUtils.cpp -o StatUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/QualitySample.cpp -o QualitySample.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/LengthHistogram.cpp -o LengthHistogram.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSet.cpp -o ContextSet.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSample.cpp -o ContextSample.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c qvs/QualityValueProfile.cpp -o QualityValueProfile.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SummaryPrinter.cpp -o SummaryPrinter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SAMPrinter.cpp -o SAMPrinter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/IntervalPrinter.cpp -o IntervalPrinter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/CCSIterator.cpp -o CCSIterator.shared.o files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool, bool)': files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] } catch (std::exception e) { ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:8, from files/ReaderAgglomerate.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:360:50: required from here ../hdf/HDFBasReader.hpp:602:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:401:50: required from here ../hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:516:50: required from here ../hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ ../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]': files/ReaderAgglomerate.cpp:611:64: required from here ../hdf/HDFBasReader.hpp:691:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ In file included from ../alignment/files/ReaderAgglomerate.hpp:9, from files/ReaderAgglomerate.cpp:1: ../hdf/HDFCCSReader.hpp: In instantiation of 'int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]': files/ReaderAgglomerate.cpp:664:50: required from here ../hdf/HDFCCSReader.hpp:270:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/BaseSequenceIO.cpp -o BaseSequenceIO.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/MatchPos.cpp -o MatchPos.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/ClusterList.cpp -o ClusterList.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.shared.o files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)': files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=] std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl; ^~~~ files/ReaderAgglomerate.cpp:626:9: note: here case FileType::Fourbit: ^~~~ files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)': files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=] std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl; ^~~~ files/ReaderAgglomerate.cpp:671:9: note: here case FileType::Fourbit: ^~~~ g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/CmpFile.cpp -o CmpFile.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/Alignment.cpp -o Alignment.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/qsufsort.cpp -o qsufsort.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/Coordinate.cpp -o Coordinate.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.shared.o g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c MappingMetrics.cpp -o MappingMetrics.shared.o ar rc libblasr.a RegionUtils.o RangeUtils.o PhredUtils.o LogUtils.o FileOfFileNames.o BlasrFileUtils.o TupleMetrics.o DNATuple.o BaseTuple.o pdfs.o cdfs.o StatUtils.o LookupAnchorDistribution.o QualitySample.o LengthHistogram.o ContextSet.o ContextSample.o QualityValueProfile.o SequentialZmwGroupQuery.o PbiFilterZmwGroupQuery.o SummaryPrinter.o SAMPrinter.o SAMHeaderPrinter.o IntervalPrinter.o CompareSequencesPrinter.o ReaderAgglomerate.o FragmentCCSIterator.o CCSIterator.o BaseSequenceIO.o WeightedInterval.o MatchPos.o ClusterList.o AnchorParameters.o SAMSupplementalQVList.o SAMQVConversion.o SAMToAlignmentCandidateAdapter.o FilterCriteria.o CmpFile.o AlignmentStats.o AlignmentMap.o AlignmentContext.o AlignmentCandidate.o Alignment.o qsufsort.o MultikeyQuicksort.o LightweightSuffixArray.o DifferenceCovers.o FindMaxInterval.o Coordinate.o ClusterProbability.o BWTSearch.o SparseDynamicProgramming.o SDPFragment.o StringToScoreMatrix.o ScoreMatrices.o QualityValueScoreFunction.o KBandAlign.o IDSScoreFunction.o GuidedAlign.o ExtendAlign.o BaseScoreFunction.o AlignmentUtils.o MappingMetrics.o g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L../hdf/ -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o libblasr.so -Wl,-soname,libblasr.so RegionUtils.shared.o RangeUtils.shared.o PhredUtils.shared.o LogUtils.shared.o FileOfFileNames.shared.o BlasrFileUtils.shared.o TupleMetrics.shared.o DNATuple.shared.o BaseTuple.shared.o pdfs.shared.o cdfs.shared.o StatUtils.shared.o LookupAnchorDistribution.shared.o QualitySample.shared.o LengthHistogram.shared.o ContextSet.shared.o ContextSample.shared.o QualityValueProfile.shared.o SequentialZmwGroupQuery.shared.o PbiFilterZmwGroupQuery.shared.o SummaryPrinter.shared.o SAMPrinter.shared.o SAMHeaderPrinter.shared.o IntervalPrinter.shared.o CompareSequencesPrinter.shared.o ReaderAgglomerate.shared.o FragmentCCSIterator.shared.o CCSIterator.shared.o BaseSequenceIO.shared.o WeightedInterval.shared.o MatchPos.shared.o ClusterList.shared.o AnchorParameters.shared.o SAMSupplementalQVList.shared.o SAMQVConversion.shared.o SAMToAlignmentCandidateAdapter.shared.o FilterCriteria.shared.o CmpFile.shared.o AlignmentStats.shared.o AlignmentMap.shared.o AlignmentContext.shared.o AlignmentCandidate.shared.o Alignment.shared.o qsufsort.shared.o MultikeyQuicksort.shared.o LightweightSuffixArray.shared.o DifferenceCovers.shared.o FindMaxInterval.shared.o Coordinate.shared.o ClusterProbability.shared.o BWTSearch.shared.o SparseDynamicProgramming.shared.o SDPFragment.shared.o StringToScoreMatrix.shared.o ScoreMatrices.shared.o QualityValueScoreFunction.shared.o KBandAlign.shared.o IDSScoreFunction.shared.o GuidedAlign.shared.o ExtendAlign.shared.o BaseScoreFunction.shared.o AlignmentUtils.shared.o MappingMetrics.shared.o -lpbbam -lpbbam -lpbdata -lpbihdf make[4]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/alignment' make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' make[2]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' make[1]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg' /usr/bin/make -k gtest make[2]: Entering directory '/build/pbseqlib-5.3.1+dfsg' /usr/bin/make -C /build/pbseqlib-5.3.1+dfsg//unittest gtest make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/unittest' make[3]: *** No rule to make target 'gtest-all.o', needed by 'libblasr-test-runner'. make[3]: *** No rule to make target 'gtest_main.o', needed by 'libblasr-test-runner'. g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSSequence_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/CCSSequence_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/CCSSequence_gtest.cpp:25:10: fatal error: pbdata/CCSSequence.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: CCSSequence_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTASequence_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTASequence_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTASequence_gtest.cpp:25:10: fatal error: pbdata/FASTASequence.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FASTASequence_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SeqUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/SeqUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/SeqUtils_gtest.cpp:22:10: fatal error: pbdata/SeqUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: SeqUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o DNASequence_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/DNASequence_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/DNASequence_gtest.cpp:26:10: fatal error: pbdata/DNASequence.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: DNASequence_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o defs_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/defs_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/defs_gtest.cpp:21:10: fatal error: pbdata/defs.h: No such file or directory #include ^~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: defs_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o NucConversion_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/NucConversion_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/NucConversion_gtest.cpp:21:10: fatal error: pbdata/NucConversion.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: NucConversion_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQReader_gtest.cpp:22:10: fatal error: pbdata/FASTQReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FASTQReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o VectorUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/VectorUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/VectorUtils_gtest.cpp:23:10: fatal error: pbdata/VectorUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: VectorUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ScanData_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/ScanData_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/ScanData_gtest.cpp:21:10: fatal error: pbdata/reads/ScanData.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: ScanData_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ChangeListID_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/ChangeListID_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/ChangeListID_gtest.cpp:23:10: fatal error: pbdata/ChangeListID.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: ChangeListID_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o utils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils_gtest.cpp:24:10: fatal error: pbdata/utils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: utils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTSequence_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/SMRTSequence_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/SMRTSequence_gtest.cpp:24:10: fatal error: pbdata/SMRTSequence.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: SMRTSequence_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTAReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTAReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTAReader_gtest.cpp:22:10: fatal error: pbdata/FASTAReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FASTAReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQSequence_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQSequence_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQSequence_gtest.cpp:25:10: fatal error: pbdata/FASTQSequence.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FASTQSequence_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o StringUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/StringUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/StringUtils_gtest.cpp:20:10: fatal error: pbdata/StringUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: StringUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTTitle_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils/SMRTTitle_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils/SMRTTitle_gtest.cpp:3:10: fatal error: pbdata/utils/SMRTTitle.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: SMRTTitle_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o TitleTable_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/metagenome/TitleTable_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/metagenome/TitleTable_gtest.cpp:22:10: fatal error: pbdata/metagenome/TitleTable.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: TitleTable_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RefInfo_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/RefInfo_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/RefInfo_gtest.cpp:21:10: fatal error: pbdata/saf/RefInfo.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: RefInfo_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlnGroup_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/AlnGroup_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/AlnGroup_gtest.cpp:21:10: fatal error: pbdata/saf/AlnGroup.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: AlnGroup_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o MovieInfo_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/MovieInfo_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/MovieInfo_gtest.cpp:21:10: fatal error: pbdata/Types.h: No such file or directory #include ^~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: MovieInfo_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionAnnotations_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionAnnotations_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionAnnotations_gtest.cpp:27:10: fatal error: pbdata/reads/ReadInterval.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: RegionAnnotations_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReadType_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/ReadType_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/ReadType_gtest.cpp:21:10: fatal error: pbdata/reads/ReadType.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: ReadType_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionTypeMap_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionTypeMap_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionTypeMap_gtest.cpp:25:10: fatal error: pbdata/reads/RegionTypeMap.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: RegionTypeMap_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o QualityValueVector_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/qvs/QualityValueVector_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/pbdata/qvs/QualityValueVector_gtest.cpp:21:10: fatal error: pbdata/qvs/QualityValue.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: QualityValueVector_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFUtils_gtest.cpp:22:10: fatal error: hdf/HDFUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataWriter_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataWriter_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataWriter_gtest.cpp:23:10: fatal error: hdf/HDFFile.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFScanDataWriter_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFCCSReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFCCSReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFCCSReader_gtest.cpp:22:10: fatal error: hdf/HDFCCSReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFCCSReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFPlsReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFPlsReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFPlsReader_gtest.cpp:22:10: fatal error: hdf/HDFPlsReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFPlsReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataReader_gtest.cpp:4:10: fatal error: hdf/HDFScanDataReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFScanDataReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFBasReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFBasReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFBasReader_gtest.cpp:22:10: fatal error: hdf/HDFBasReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFBasReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDF2DArray_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDF2DArray_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDF2DArray_gtest.cpp:24:10: fatal error: hdf/HDF2DArray.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDF2DArray_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFZMWReader_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFZMWReader_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFZMWReader_gtest.cpp:22:10: fatal error: hdf/HDFZMWReader.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: HDFZMWReader_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RangeUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RangeUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RangeUtils_gtest.cpp:21:10: fatal error: alignment/utils/RangeUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: RangeUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FileUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/FileUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/FileUtils_gtest.cpp:21:10: fatal error: alignment/utils/FileUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FileUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionUtils_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RegionUtils_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RegionUtils_gtest.cpp:22:10: fatal error: alignment/utils/RegionUtils.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: RegionUtils_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o PbiFilterZmwGroupQuery_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:5:10: fatal error: alignment/query/PbiFilterZmwGroupQuery.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: PbiFilterZmwGroupQuery_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SequentialZmwGroupQuery_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:5:10: fatal error: alignment/query/SequentialZmwGroupQuery.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: SequentialZmwGroupQuery_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlignmentMap_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp:25:10: fatal error: alignment/datastructures/alignment/AlignmentMap.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: AlignmentMap_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CmpIndexedStringTable_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp:21:10: fatal error: alignment/datastructures/alignment/CmpIndexedStringTable.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: CmpIndexedStringTable_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSIterator_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/CCSIterator_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/CCSIterator_gtest.cpp:22:10: fatal error: alignment/files/CCSIterator.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: CCSIterator_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReaderAgglomerate_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/ReaderAgglomerate_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25:10: fatal error: alignment/files/ReaderAgglomerate.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: ReaderAgglomerate_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_other_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:27:10: fatal error: alignment/files/CCSIterator.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FragmentCCSIterator_other_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_gtest.cpp:26:10: fatal error: alignment/files/FragmentCCSIterator.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: FragmentCCSIterator_gtest.o] Error 1 g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/build/pbseqlib-5.3.1+dfsg/unittest/ -I/build/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SAMPrinter_gtest.o /build/pbseqlib-5.3.1+dfsg/unittest/alignment/format/SAMPrinter_gtest.cpp /build/pbseqlib-5.3.1+dfsg/unittest/alignment/format/SAMPrinter_gtest.cpp:29:10: fatal error: alignment/format/SAMPrinter.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [makefile:108: SAMPrinter_gtest.o] Error 1 make[3]: Target 'gtest' not remade because of errors. make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/unittest' make[2]: *** [makefile:27: gtest] Error 2 make[2]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' make[1]: [debian/rules:37: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg' mkdir -p debian/libpbdata-dev/usr/include/pbseq cp -r pbdata debian/libpbdata-dev/usr/include/pbseq/ mkdir -p debian/libpbihdf-dev/usr/include/pbseq/ cp -r hdf debian/libpbihdf-dev/usr/include/pbseq/ mkdir -p debian/libblasr-dev/usr/include/pbseq/ cp -r alignment debian/libblasr-dev/usr/include/pbseq/ find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete find debian/*/usr/include/ -name "*.mk" -delete dh_auto_install make[1]: Leaving directory '/build/pbseqlib-5.3.1+dfsg' dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libpbihdf/usr/lib/aarch64-linux-gnu/libpbihdf.so (ELF format: 'elf64-littleaarch64' abi: '020100b700000000'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libblasr/usr/lib/aarch64-linux-gnu/libblasr.so (ELF format: 'elf64-littleaarch64' abi: '020100b700000000'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libpbihdf.so needed by debian/libblasr/usr/lib/aarch64-linux-gnu/libblasr.so (ELF format: 'elf64-littleaarch64' abi: '020100b700000000'; RPATH: '') dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libblasr-dbgsym' in '../libblasr-dbgsym_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.1+dfsg-2.1_all.deb'. dpkg-deb: building package 'libpbihdf' in '../libpbihdf_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.1+dfsg-2.1_all.deb'. dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libpbdata' in '../libpbdata_5.3.1+dfsg-2.1_arm64.deb'. dpkg-deb: building package 'libblasr' in '../libblasr_5.3.1+dfsg-2.1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbseqlib_5.3.1+dfsg-2.1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/27219 and its subdirectories I: Current time: Thu Sep 16 05:56:18 -12 2021 I: pbuilder-time-stamp: 1631814978