Sun Aug 22 20:23:56 UTC 2021 I: starting to build pbseqlib/bullseye/arm64 on jenkins on '2021-08-22 20:23' Sun Aug 22 20:23:56 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_28/38661/console.log Sun Aug 22 20:23:56 UTC 2021 I: Downloading source for bullseye/pbseqlib=5.3.4+dfsg-3 --2021-08-22 20:23:56-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pbseqlib/pbseqlib_5.3.4%2bdfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2448 (2.4K) Saving to: ‘pbseqlib_5.3.4+dfsg-3.dsc’ 0K .. 100% 135M=0s 2021-08-22 20:23:56 (135 MB/s) - ‘pbseqlib_5.3.4+dfsg-3.dsc’ saved [2448/2448] Sun Aug 22 20:23:56 UTC 2021 I: pbseqlib_5.3.4+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbseqlib Binary: libblasr-dev, libblasr5.3.4, libpbseq, libpbseq-dev, libpbdata-dev, libpbihdf-dev Architecture: any Version: 5.3.4+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr_libcpp Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pbseqlib Vcs-Git: https://salsa.debian.org/med-team/pbseqlib.git Build-Depends: debhelper-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbcopper-dev, libhts-dev Package-List: libblasr-dev deb libdevel optional arch=any libblasr5.3.4 deb libs optional arch=any libpbdata-dev deb libdevel optional arch=any libpbihdf-dev deb libdevel optional arch=any libpbseq deb science optional arch=any libpbseq-dev deb libdevel optional arch=any Checksums-Sha1: 91705f34f5eebd45a507a1021b28c4f5d20342d6 957612 pbseqlib_5.3.4+dfsg.orig.tar.xz b57f398923baaa2212242f62d6d972b26f26b1b6 9444 pbseqlib_5.3.4+dfsg-3.debian.tar.xz Checksums-Sha256: 5cfda4a8a3ee9264945234d186e20f2a470e8f0270300037d4c7b205c00797fc 957612 pbseqlib_5.3.4+dfsg.orig.tar.xz 4bd2cb2e52b1c82e3de45f33b1e47eefe24319ac1f9e63822320658601ec4e1d 9444 pbseqlib_5.3.4+dfsg-3.debian.tar.xz Files: 89e242da1d862ddfaee04b463509f9f1 957612 pbseqlib_5.3.4+dfsg.orig.tar.xz 28422264d3770b708c77d3e98bf5b0f8 9444 pbseqlib_5.3.4+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+ydfQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGXYw/+PmeflT4Crm76trWy5+yaHfvCJauBQlM1 bzf0LXNGYeiNu9n05ItWjhGD4NgjosI4MjCMwVwRo5dSSIDCHAE6FSsK1x6i6YPj ygzFHB9GGQ0n4aYh1dRgpvn8XqM5YI6c5RE9wZrmXlDdjaE2OxRqeH9Mfgpu5jdt hqfRatlKxsZFyZJlsV4BSaGWy+Ul5kF4n/sPKzV07prmgxfHfJaKl22OIvwrSBtO q8T5NkLift+Ob1uStZ62qthjI8yjlD5Skg13RhYC6TF0Ab9u2mACrRm6z6ipatBq f91mN8osXqrBcAYI9AlnMDXCTQd1tt/MkbrZmfozQcl4DjQ8CVokDbk20v+nvuiq bU6U3664lQ3x2Xw4+BAoZxY5Q/3EvDAMTFJYY97bvDAZk3RL95AbHwRbQ8dvU/bz 91K1BO8L+sK2kRxWCFCdF5a1uTtWhz4YV0zHw+KTDrO6wiAQZ4f5FQ7Q1KcC67zr eeuupZFJeXv+djQ2msL+24FUR+Z9u88R9BPExAqOXDlfIXWEV7EHz/XtqbM6yIv5 sIZPX7MYuSW61qtJH0Hrm0W6HMegAkViPOehROtVrS13B18LWORt0mHSHNhE2Ag3 IS62X+tZpsgFaPt8SvQhAAuYu2NDxFwUYj8lvTRdQ0DopSfXPu3XyyUxBCy0TMC+ 4paFTQ5mRto= =YKgE -----END PGP SIGNATURE----- Sun Aug 22 20:23:56 UTC 2021 I: Checking whether the package is not for us Sun Aug 22 20:23:56 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Sun Aug 22 20:23:56 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Sun Aug 22 20:32:41 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 24 14:46:58 -12 2022 I: pbuilder-time-stamp: 1664074018 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_5.3.4+dfsg-3.dsc] I: copying [./pbseqlib_5.3.4+dfsg.orig.tar.xz] I: copying [./pbseqlib_5.3.4+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.wasmD_XX/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 16 00:52:04 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.4+dfsg-3.dsc dpkg-source: info: extracting pbseqlib in pbseqlib-5.3.4+dfsg dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg.orig.tar.xz dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg-3.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 dpkg-source: info: applying meson.patch dpkg-source: info: applying static+shared_lib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8904/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,-fixfilepath 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='8904' 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.Zpqd6PfdUS/pbuilderrc_GUSa --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/b1 --logfile b1/build.log pbseqlib_5.3.4+dfsg-3.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 codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 2021 more -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 23 03:47 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/8904/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-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbcopper-dev, libhts-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 ... 19646 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on googletest; however: Package googletest is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev 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 libpbcopper-dev; however: Package libpbcopper-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-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} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{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} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgtest-dev{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp24{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam1.6.0{a} libpbcopper-dev{a} libpbcopper1.8.0{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} pkg-config{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3-pkg-resources{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 57.5 MB of archives. After unpacking 329 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 d-shlibs all 0.98 [17.9 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 googletest all 1.10.0.20201025-1.1 [629 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 hdf5-helpers arm64 1.10.6+repack-4 [40.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libaec0 arm64 1.0.4-1 [19.8 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libsz2 arm64 1.0.4-1 [6736 B] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libaec-dev arm64 1.0.4-1 [18.2 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libgtest-dev arm64 1.10.0.20201025-1.1 [221 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libhdf5-103-1 arm64 1.10.6+repack-4 [1032 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libhdf5-cpp-103-1 arm64 1.10.6+repack-4 [131 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libhdf5-fortran-102 arm64 1.10.6+repack-4 [103 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-100 arm64 1.10.6+repack-4 [78.6 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-fortran-100 arm64 1.10.6+repack-4 [55.0 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-cpp-100 arm64 1.10.6+repack-4 [37.6 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo-dev arm64 1:2.0.6-4 [255 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libjpeg-dev arm64 1:2.0.6-4 [67.8 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libhdf5-dev arm64 1.10.6+repack-4 [2535 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libpbcopper1.8.0 arm64 1.8.0+dfsg-2+b1 [371 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libpbbam1.6.0 arm64 1.6.0+dfsg-2 [611 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 libssl-dev arm64 1.1.1k-1 [1689 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libpbbam-dev arm64 1.6.0+dfsg-2 [87.2 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libpbcopper-dev arm64 1.8.0+dfsg-2+b1 [640 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 ninja-build arm64 1.10.1-1 [107 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 meson all 0.56.2-1 [437 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Fetched 57.5 MB in 1s (52.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../4-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 20934 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../01-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:arm64. Preparing to unpack .../02-libprocps8_2%3a3.3.17-5_arm64.deb ... Unpacking libprocps8:arm64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.17-5_arm64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../06-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../09-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../15-cmake-data_3.18.4-2_all.deb ... Unpacking cmake-data (3.18.4-2) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../16-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../17-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../18-libarchive13_3.4.3-2+b1_arm64.deb ... Unpacking libarchive13:arm64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../19-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../20-libsasl2-modules-db_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../21-libsasl2-2_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../22-libldap-2.4-2_2.4.57+dfsg-3_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../23-libnghttp2-14_1.43.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.43.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../24-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../25-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../26-libssh2-1_1.9.0-2_arm64.deb ... Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../27-libcurl4_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl4:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libjsoncpp24:arm64. Preparing to unpack .../28-libjsoncpp24_1.9.4-4_arm64.deb ... Unpacking libjsoncpp24:arm64 (1.9.4-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../29-librhash0_1.4.1-2_arm64.deb ... Unpacking librhash0:arm64 (1.4.1-2) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../30-libuv1_1.40.0-2_arm64.deb ... Unpacking libuv1:arm64 (1.40.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../31-cmake_3.18.4-2_arm64.deb ... Unpacking cmake (3.18.4-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../32-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../33-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../34-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../35-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../36-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../37-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../38-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../39-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../40-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../42-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../43-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../44-po-debconf_1.0.21+nmu1_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/pbseqlib-5.3.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbseqlib_5.3.4+dfsg-3_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbseqlib-5.3.4+dfsg' dh_auto_clean find -name defines.mk -delete rm -f pbdata/libconfig.h make[1]: Leaving directory '/build/pbseqlib-5.3.4+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu The Meson build system Version: 0.56.2 Source dir: /build/pbseqlib-5.3.4+dfsg Build dir: /build/pbseqlib-5.3.4+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: libblasr Project version: 5.3.4 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial' C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial' Host machine cpu family: aarch64 Host machine cpu: aarch64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Run-time dependency pbbam found: YES 1.6.0 Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-4 Library rt found: YES WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.49.0': disabler arg in dependency. Run-time dependency HDF5 for cpp found: YES 1.10.6 Configuring LibBlasrConfig.h using configuration Program tools/check-formatting found: YES (/build/pbseqlib-5.3.4+dfsg/tools/check-formatting) WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.53.0': Fallback without variable name. Run-time dependency GTest found: YES 1.10.0 Build targets in project: 3 WARNING: Project specifies a minimum meson_version '>= 0.46.0' but uses features which were added in newer versions: * 0.49.0: {'disabler arg in dependency'} * 0.53.0: {'Fallback without variable name'} Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -v [1/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp ../hdf/HDFAttributable.cpp: In member function ‘int HDFAttributable::ContainsAttribute(const string&)’: ../hdf/HDFAttributable.cpp:48:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 48 | } catch (H5::Exception e) { | ^ [2/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:82:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 82 | DEFINE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:83:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 83 | DEFINE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:84:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 84 | DEFINE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:85:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 85 | DEFINE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:86:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 86 | DEFINE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:87:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 87 | DEFINE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:88:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 88 | DEFINE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [3/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [4/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp [5/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:9:92: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 9 | attribute = object.createAttribute(atomName.c_str(), strType, H5::DataSpace(H5S_SCALAR)); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:20:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 20 | DEFINE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:21:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 21 | DEFINE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:22:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 22 | DEFINE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:23:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 23 | DEFINE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:24:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 24 | DEFINE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:25:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 25 | DEFINE_TYPED_CREATE_ATOM(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:26:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 26 | DEFINE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [6/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp ../hdf/HDFData.cpp: In member function ‘int HDFData::BaseInitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:37:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 37 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/HDFData.cpp: In member function ‘int HDFData::InitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:52:59: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 52 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [7/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:67:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 67 | DEFINE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:68:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 68 | DEFINE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char*]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:69:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 69 | DEFINE_TYPED_CREATE_ARRAY(char *, H5::StrType(0, H5T_VARIABLE)) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:70:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 70 | DEFINE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:71:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 71 | DEFINE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:72:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 72 | DEFINE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:73:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 73 | DEFINE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string]’: ../hdf/BufferedHDFArray.cpp:79:86: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), varStrType, space, cparms); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [8/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFAlnGroupGroup.hpp:6, from ../hdf/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:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ ../hdf/HDFAlnGroupGroup.cpp:16:29: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } 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:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ ../hdf/HDFAlnGroupGroup.cpp:18:25: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [9/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:23:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 23 | } catch (FileIException e) { | ^ ../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:34:75: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ ../hdf/HDFFile.cpp:35:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 35 | } catch (FileIException fileException) { | ^~~~~~~~~~~~~ [10/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp ../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’: ../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 18 | group = fg.openGroup(groupName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFGroup.hpp:9, from ../hdf/HDFGroup.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ [11/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp [12/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp [13/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAlnInfoGroup.cpp:44:77: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [14/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp [15/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp ../hdf/HDFBaseCallsWriter.cpp: In member function ‘virtual void HDFBaseCallsWriter::Close()’: ../hdf/HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 364 | } catch (H5::Exception e) { | ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:12, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFBaseCallsWriter.cpp:342:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: ../hdf/HDFBaseCallsWriter.cpp:350:35: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [16/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFCmpExperimentGroup.hpp:10, from ../hdf/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:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned char]’ ../hdf/HDFCmpExperimentGroup.cpp:36:69: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } 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:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = char]’ ../hdf/HDFCmpExperimentGroup.cpp:199:72: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [17/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [18/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp [19/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp ../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: ../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 44 | for (auto annotation : annotations) | ^~~~~~~~~~~ In file included from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFWriterBase.hpp:17, from ../hdf/HDFRegionsWriter.hpp:13, from ../hdf/HDFRegionsWriter.cpp:3: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [20/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../hdf/HDFRegionTableReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFRegionTableReader.cpp:31:54: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../hdf/HDFRegionTableReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [21/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:26:67: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:29:67: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:33:75: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [22/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp [23/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [24/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [25/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp [26/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFWriterBase.cpp:49:88: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [27/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp [28/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp ../hdf/HDFPulseCallsWriter.cpp: In member function ‘virtual void HDFPulseCallsWriter::Close()’: ../hdf/HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 513 | } catch (H5::Exception e) { | ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFPulseCallsWriter.hpp:12, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFPulseCallsWriter.cpp:492:47: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: ../hdf/HDFPulseCallsWriter.cpp:497:39: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: 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]’: ../hdf/HDFPulseCallsWriter.cpp:498:49: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [29/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWMetricsWriter.hpp:7, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: ../hdf/HDFZMWMetricsWriter.cpp:54:27: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFZMWMetricsWriter.cpp:55:30: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWMetricsWriter.hpp:8, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWMetricsWriter.hpp:6, from ../hdf/HDFZMWMetricsWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [30/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [31/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp [32/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp [33/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWWriter.hpp:11, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: ../hdf/HDFZMWWriter.cpp:149:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFZMWWriter.cpp:151:28: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWWriter.hpp:12, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWWriter.hpp:10, from ../hdf/HDFZMWWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [34/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp [35/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from ../alignment/algorithms/alignment/ExtendAlign.hpp:6, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [36/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp [37/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp [38/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from ../alignment/algorithms/alignment/GuidedAlign.hpp:6, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [39/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp [40/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from ../alignment/algorithms/alignment/KBandAlign.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [41/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp [42/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp [43/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp [44/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp [45/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp [46/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp [47/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp [48/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp [49/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/10/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFBasReader.hpp:21, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of ‘void T_HDFBasReader::GetMinMaxHoleNumber(UInt&, UInt&) [with T_Sequence = FASTASequence; UInt = unsigned int]’: ../hdf/HDFUtils.cpp:41:55: required from here ../hdf/HDFBasReader.hpp:1233:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 1233 | assert(nReads >= 0); | ~~~~~~~^~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFUtils.cpp:39:38: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [50/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp [51/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp [52/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp [53/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp ../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: ../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); | ^~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/datastructures/alignment/Alignment.cpp:2: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ [54/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp [55/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp [56/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp [57/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp [58/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp [59/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp [60/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp [61/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -c ../alignment/datastructures/alignment/FilterCriteria.cpp [62/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp [63/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp [64/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp [65/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp [66/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from ../alignment/format/CompareSequencesPrinter.hpp:4, from ../alignment/format/CompareSequencesPrinter.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [67/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp [68/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp [69/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o -MF libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o -c ../alignment/qvs/QualityValueProfile.cpp [70/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o -c ../alignment/format/SAMPrinter.cpp [71/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/10/cassert:44, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, from ../alignment/simulator/LengthHistogram.hpp:8, from ../alignment/simulator/LengthHistogram.cpp:1: ../alignment/simulator/CDFMap.hpp: In instantiation of ‘int CDFMap::SelectRandomValue(T_Data&) [with T_Data = int]’: ../alignment/simulator/LengthHistogram.cpp:27:94: required from here ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ [72/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp 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-fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp [93/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time 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libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp [95/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp [96/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp [97/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp [98/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp [99/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp [100/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp [101/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp [102/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [103/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o -c ../pbdata/reads/RegionAnnotation.cpp [104/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp [105/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp [106/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp [107/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp [108/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp [109/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { | ^~~~~~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::RegionAnnotationsOfType(RegionType) const’: ../pbdata/reads/RegionAnnotations.cpp:37:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 37 | for (auto ra : table_) | ^~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘RegionAnnotation RegionAnnotations::TheHQRegion() const’: ../pbdata/reads/RegionAnnotations.cpp:65:22: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 65 | return hqs_[0]; | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ In file included from ../pbdata/reads/RegionAnnotations.cpp:3: ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] 8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ | ^~~ ../pbdata/reads/RegionAnnotations.cpp:67:9: note: in expansion of macro ‘BLASR_THROW’ 67 | BLASR_THROW("Zmw has more than one HQRegion"); | ^~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this ‘else’ clause 66 | else | ^~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::AdapterIntervals() const’: ../pbdata/reads/RegionAnnotations.cpp:84:34: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 84 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::SubreadIntervals(DNALength, bool, bool) const’: ../pbdata/reads/RegionAnnotations.cpp:102:42: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 102 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp:121:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 121 | for (auto insert : inserts) { | ^~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [110/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp [111/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp [112/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o -c ../pbdata/reads/BaseFile.cpp [113/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp [114/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp [115/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp [116/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::Initialize(bool, bool)’: ../alignment/files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 267 | } catch (std::exception e) { | ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:360:50: required from here ../hdf/HDFBasReader.hpp:602:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 602 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:401:50: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:516:50: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:611:64: required from here ../hdf/HDFBasReader.hpp:691:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 691 | } catch (H5::DataSetIException e) { | ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:9, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: ../alignment/files/ReaderAgglomerate.cpp:664:50: required from here ../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 270 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../alignment/files/ReaderAgglomerate.cpp:250:56: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)’: ../alignment/files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=] 624 | std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl; | ^~~~ ../alignment/files/ReaderAgglomerate.cpp:626:9: note: here 626 | case FileType::Fourbit: | ^~~~ ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::GetNext(CCSSequence&)’: ../alignment/files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=] 669 | std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl; | ^~~~ ../alignment/files/ReaderAgglomerate.cpp:671:9: note: here 671 | case FileType::Fourbit: | ^~~~ [117/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp [118/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp [119/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp [120/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o -c ../pbdata/utils/SMRTTitle.cpp [121/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o -c ../pbdata/sam/SAMKeywordValuePair.cpp [122/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o -c ../pbdata/utils/TimeUtils.cpp [123/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o -c ../pbdata/sam/SAMAlignment.cpp [124/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o -MF libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o -c ../pbdata/ChangeListID.cpp [125/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp [126/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp [127/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o -MF libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o -c ../pbdata/NucConversion.cpp [128/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o -c ../pbdata/GFFFile.cpp [129/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp [130/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp In file included from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/FASTASequence.hpp: In instantiation of ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = FASTASequence; _Args = {FASTASequence}]’: /usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]’ /usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*]’ /usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]’ /usr/include/c++/10/bits/stl_uninitialized.h:347:2: required from ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator]’ /usr/include/c++/10/bits/vector.tcc:659:48: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ /usr/include/c++/10/bits/stl_vector.h:940:4: required from ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ ../pbdata/BlasrFASTAReader.cpp:441:26: required from here ../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] 19 | class FASTASequence : public DNASequence | ^~~~~~~~~~~~~ In file included from ../pbdata/FASTASequence.hpp:13, from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ 51 | DNASequence &operator=(const DNASequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/bits/alloc_traits.h:33, from /usr/include/c++/10/ext/alloc_traits.h:34, from /usr/include/c++/10/bits/basic_string.h:40, from /usr/include/c++/10/string:55, from ../pbdata/FASTAReader.hpp:5, from ../pbdata/BlasrFASTAReader.cpp:2: /usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [131/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o -c ../pbdata/MD5Utils.cpp [132/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp [133/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp [134/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp [135/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp [136/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [137/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp [139/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp [140/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp In file included from ../pbdata/SMRTSequence.cpp:3: ../pbdata/SMRTSequence.cpp: In member function ‘float SMRTSequence::HQRegionSnr(char) const’: ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] 8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ | ^~~ ../pbdata/SMRTSequence.cpp:329:9: note: in expansion of macro ‘BLASR_THROW’ 329 | BLASR_THROW("Base must be in A, C, G, T"); | ^~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this ‘else’ clause 328 | else | ^~~~ ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: ../pbdata/SMRTSequence.cpp:353:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 353 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:378:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 378 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ [141/187] c++ -o libblasr.so.5.3.4 libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.4 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lrt /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [142/187] /usr/bin/meson --internal symbolextractor /build/pbseqlib-5.3.4+dfsg/obj-aarch64-linux-gnu libblasr.so.5.3.4 libblasr.so.5.3.4 libblasr.so.5.3.4.p/libblasr.so.5.3.4.symbols [143/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o [144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp [148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp [149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp [150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp [151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp [152/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp [153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp [157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp [159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp [161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp [162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp [164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: ../hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp [168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -c ../unittest/pbdata/reads/RegionTypeMap_gtest.cpp [169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp In file included from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 270 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ ../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFCCSReader.hpp:93:57: required from ‘int HDFCCSReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:39:5: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp [171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp [172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp [173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp In file included from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ ../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFBasReader_gtest.cpp:33:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp [175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp [177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp [179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp [180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp [181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp [182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const string&, const UInt&, DNALength, DNALength, const string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 66 | return smrt; | ^~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymerase_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:133:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:133:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletion_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:192:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:192:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletionNoSubstitution_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:246:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:246:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ [183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp [184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -c ../unittest/pbdata/DNASequence_gtest.cpp [187/187] c++ -o unittest/libblasr_unittest unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now -Wl,--start-group libblasr.so.5.3.4 /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lrt /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/aarch64-linux-gnu/libgtest_main.a -lpthread /usr/lib/aarch64-linux-gnu/libgtest.a -Wl,--end-group '-Wl,-rpath,$ORIGIN/..' -Wl,-rpath-link,/build/pbseqlib-5.3.4+dfsg/obj-aarch64-linux-gnu/ debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbseqlib-5.3.4+dfsg' /usr/bin/make -k gtest make[2]: Entering directory '/build/pbseqlib-5.3.4+dfsg' make[2]: *** No rule to make target 'gtest'. make[2]: Leaving directory '/build/pbseqlib-5.3.4+dfsg' make[1]: [debian/rules:31: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/build/pbseqlib-5.3.4+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && DESTDIR=/build/pbseqlib-5.3.4\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing libblasr.so.5.3.4 to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu Installing libblasr.a to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu Installing /build/pbseqlib-5.3.4+dfsg/obj-aarch64-linux-gnu/LibBlasrConfig.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr Installing /build/pbseqlib-5.3.4+dfsg/hdf/BufferedHDF2DArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/BufferedHDF2DArrayImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/BufferedHDFArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/BufferedHDFArrayImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/DatasetCollection.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/DatasetCollectionImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDF2DArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFAlnGroupGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFAlnGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFAlnInfoGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFAtom.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFAttributable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFBaseCallsWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFBasReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFBasWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFBaxWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCCSReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpData.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpExperimentGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpRefAlignmentGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpRootGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCmpSupportedFields.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFCommonFG.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFConfig.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFData.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFFileLogGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFMovieInfoGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFNewBasReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFPlsReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFPlsWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFPulseCallsWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFPulseDataFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFPulseWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFRefGroupGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFRefInfoGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFRegionsWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFRegionTableReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFRegionTableWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFScanDataReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFScanDataWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFSentinalFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFSMRTSequenceReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFWriteBuffer.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFWriterBase.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFZMWMetricsWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFZMWReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/hdf/HDFZMWWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/FragmentSort.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPColumn.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPFragment.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPSet.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AffineGuidedAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AffineKBandAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentFormats.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/BaseScoreFunction.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/ExtendAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/FullQVAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GraphPaper.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GraphPaperImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GuidedAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/IDSScoreFunction.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/KBandAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/OneGapAlignment.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/QualityValueScoreFunction.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/ScoreMatrices.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SDPAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SDPAlignImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/StringToScoreMatrix.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SWAlign.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SWAlignImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BasicEndpoint.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BasicEndpointImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BWTSearch.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BWTSearchImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ClusterProbability.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/Coordinate.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/FindMaxInterval.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/GlobalChain.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/GlobalChainImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValue.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueWeightor.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISQValueWeightor.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISSizeWeightor.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/MapBySuffixArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/PrioritySearchTree.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ScoreAnchors.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/compare/CompareStrings.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/compare Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/DifferenceCovers.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/Karkkainen.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/LightweightSuffixArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/MultikeyQuicksort.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/qsufsort.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-5.3.4+dfsg/alignment/bwt/BWT.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-5.3.4+dfsg/alignment/bwt/Occ.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-5.3.4+dfsg/alignment/bwt/PackedHash.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-5.3.4+dfsg/alignment/bwt/Pos.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignedPair.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentCandidate.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentContext.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentGapList.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/Alignment.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentMap.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentStats.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/ByteAlignment.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpIndexedStringTable.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpReadGroupTable.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpRefSeqTable.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/FilterCriteria.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/Path.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/SAMQVConversion.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/AnchorParameters.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/ClusterList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/MatchPos.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/WeightedInterval.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-5.3.4+dfsg/alignment/files/BaseSequenceIO.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-5.3.4+dfsg/alignment/files/CCSIterator.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-5.3.4+dfsg/alignment/files/FragmentCCSIterator.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-5.3.4+dfsg/alignment/files/ReaderAgglomerate.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-5.3.4+dfsg/alignment/files/ReaderAgglomerateImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/BAMPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/BAMPrinterImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/CompareSequencesPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/CompareSequencesPrinterImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/IntervalPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/SAMHeaderPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/SAMPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/SAMPrinterImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/StickAlignmentPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/SummaryPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/VulgarPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/format/XMLPrinter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-5.3.4+dfsg/alignment/ipc/SharedMemoryAllocator.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/ipc Installing /build/pbseqlib-5.3.4+dfsg/alignment/query/PbiFilterZmwGroupQuery.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/pbseqlib-5.3.4+dfsg/alignment/query/SequentialZmwGroupQuery.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/pbseqlib-5.3.4+dfsg/alignment/qvs/QualityValueProfile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/qvs Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/CDFMap.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextOutputList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextSample.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextSet.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/LengthHistogram.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSample.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSampleList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSampleListSet.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/simulator/QualitySample.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/AnchorDistributionTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/cdfs.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/LookupAnchorDistribution.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/pdfs.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/StatUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/StatUtilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/VarianceAccumulator.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/statistics/VarianceAccumulatorImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-5.3.4+dfsg/alignment/suffixarray/LCPTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SharedSuffixArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-5.3.4+dfsg/alignment/suffixarray/ssort.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SuffixArray.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SuffixArrayTypes.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/BaseTuple.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/CompressedDNATuple.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/CountedTuple.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATuple.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATupleImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATupleList.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/HashedTupleList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/HashedTupleListImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleCountTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleCountTableImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/tuple.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleList.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleListImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMask.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMatching.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMatchingImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMetrics.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleOperations.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleTranslations.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/FileOfFileNames.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/FileUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/LogUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/PhredUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/RangeUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/RegionUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/RegionUtilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/utils/SimpleXMLUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-5.3.4+dfsg/alignment/MappingMetrics.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment Installing /build/pbseqlib-5.3.4+dfsg/pbdata/alignment/CmpAlignment.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/pbseqlib-5.3.4+dfsg/pbdata/alignment/CmpAlignmentImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/pbseqlib-5.3.4+dfsg/pbdata/amos/AfgBasWriter.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/amos Installing /build/pbseqlib-5.3.4+dfsg/pbdata/loadpulses/MetricField.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/pbseqlib-5.3.4+dfsg/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/pbseqlib-5.3.4+dfsg/pbdata/matrix/FlatMatrix.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-5.3.4+dfsg/pbdata/matrix/FlatMatrixImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-5.3.4+dfsg/pbdata/matrix/Matrix.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-5.3.4+dfsg/pbdata/matrix/MatrixImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-5.3.4+dfsg/pbdata/metagenome/FindRandomSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-5.3.4+dfsg/pbdata/metagenome/SequenceIndexDatabase.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-5.3.4+dfsg/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-5.3.4+dfsg/pbdata/metagenome/TitleTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityTransform.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValue.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityTransform.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValue.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/AcqParams.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/BaseFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/BaseFileImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/HoleXY.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseBaseCommon.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseFileImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/ReadInterval.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/ReadType.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionAnnotation.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionAnnotations.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionTable.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionTypeMap.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/ScanData.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/reads/ZMWGroupEntry.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-5.3.4+dfsg/pbdata/saf/AlnGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-5.3.4+dfsg/pbdata/saf/AlnInfo.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-5.3.4+dfsg/pbdata/saf/MovieInfo.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-5.3.4+dfsg/pbdata/saf/RefGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-5.3.4+dfsg/pbdata/saf/RefInfo.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/AlignmentSet.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/AlignmentSetImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/CigarString.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/ReadGroup.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/ReferenceSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMAlignment.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMFlag.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMHeader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMKeywordValuePair.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMKeywordValuePairImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMReaderImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utils/BitUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utils/SMRTReadUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utils/SMRTTitle.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utils/TimeUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-5.3.4+dfsg/pbdata/CCSSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/ChangeListID.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/CommandLineParser.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/Compare4BitCompressed.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/CompressedDNASequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/CompressedSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/CompressedSequenceImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/defs.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/DNASequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/Enumerations.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/FASTAReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/FASTASequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/FASTQReader.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/FASTQSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/GFFFile.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/MD5Utils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/MD5UtilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/NucConversion.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/PacBioDefs.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/PackedDNASequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/PrettyException.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/ReverseCompressIndex.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/SeqUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/SeqUtilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/SMRTSequence.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/StringUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/Types.h to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/utilsImpl.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/pbdata/VectorUtils.hpp to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-5.3.4+dfsg/obj-aarch64-linux-gnu/meson-private/libblasr.pc to /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/build/pbseqlib-5.3.4+dfsg' dh_install -p libpbdata-dev usr/include/libblasr/pbdata usr/include/pbseq dh_install -p libpbihdf-dev usr/include/libblasr/hdf usr/include/pbseq dh_install -p libblasr-dev usr/include/libblasr/alignment 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 d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libhdf5_serial_cpp103-dev/libhdf5-dev/ \ --override s/libpbbam1.6.0-dev/libpbbam-dev/ \ --override s/libpbcopper1.8.0-dev/libpbcopper-dev/ \ --movedev debian/tmp/usr/include/libblasr usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/libblasr.so Library package automatic movement utility --> libhdf5-dev package exists. --> libpbbam-dev package exists. --> libpbcopper-dev package exists. set -e install -d -m 755 debian/libblasr-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libblasr5.3.4/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libblasr.a debian/libblasr-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libblasr.so debian/libblasr-dev/usr/lib/aarch64-linux-gnu mv /build/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libblasr.so.5.3.4 debian/libblasr5.3.4/usr/lib/aarch64-linux-gnu PKGDEV=libblasr-dev PKGSHL=libblasr5.3.4 install -d -m 755 debian/libblasr-dev/usr/include mv debian/tmp/usr/include/libblasr debian/libblasr-dev/usr/include install -d -m 755 debian/libblasr-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libblasr-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/libblasr-dev/usr/include/libblasr debian/libblasr-dev/usr/include/pbseq mv debian/libblasr-dev/usr/include/pbseq/libblasr/LibBlasrConfig.h debian/libblasr-dev/usr/include/pbseq dh_install make[1]: Leaving directory '/build/pbseqlib-5.3.4+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libblasr-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libblasr5.3.4-dbgsym' in '../libblasr5.3.4-dbgsym_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libblasr5.3.4' in '../libblasr5.3.4_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.4+dfsg-3_arm64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.4+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbseqlib_5.3.4+dfsg-3_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) dpkg-genchanges: info: not including original source code in upload 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/8904 and its subdirectories I: Current time: Sat Sep 24 14:55:37 -12 2022 I: pbuilder-time-stamp: 1664074537 Sun Aug 22 20:32:41 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Sun Aug 22 20:32:41 UTC 2021 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Sun Aug 22 20:46:33 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Sun Aug 22 20:46:34 UTC 2021 I: pbseqlib_5.3.4+dfsg-3_arm64.changes: Format: 1.8 Date: Mon, 16 Nov 2020 13:47:40 +0100 Source: pbseqlib Binary: libblasr-dev libblasr5.3.4 libblasr5.3.4-dbgsym libpbdata-dev libpbihdf-dev libpbseq libpbseq-dev Architecture: arm64 Version: 5.3.4+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libblasr-dev - tools for aligning PacBio reads to target sequences (development libblasr5.3.4 - tools for aligning PacBio reads to target sequences libpbdata-dev - tools for handling PacBio sequences (development files) libpbihdf-dev - tools for handling PacBio hdf5 files (development files) libpbseq - library for analyzing PacBio sequencing data libpbseq-dev - library for analyzing PacBio sequencing data (development files) Changes: pbseqlib (5.3.4+dfsg-3) unstable; urgency=medium . * Install LibBlasrConfig.h at correct location Checksums-Sha1: eba53962178e2795315738fde28b862a0a838b1e 2042616 libblasr-dev_5.3.4+dfsg-3_arm64.deb 0092a2e2f6f55f342ef76f5199bad35ec36a893a 8194468 libblasr5.3.4-dbgsym_5.3.4+dfsg-3_arm64.deb 020ed3fe3b1edd8289ad385b771b5183082dd3fa 1038296 libblasr5.3.4_5.3.4+dfsg-3_arm64.deb c428c98ac2a73412ee6424bfbd8c2d232c261f9d 40976 libpbdata-dev_5.3.4+dfsg-3_arm64.deb f6fe9bdb5544570a0a71abca3dd55e30737433b5 47456 libpbihdf-dev_5.3.4+dfsg-3_arm64.deb 194e2dc571d7a26cf073d6c78ed3f43c4ccd85b3 5220 libpbseq-dev_5.3.4+dfsg-3_arm64.deb b62788662355eea15eb269eee8f46f385fa9734b 5200 libpbseq_5.3.4+dfsg-3_arm64.deb 6d826e82fb54e6e69663f7ae7b62cd992cb841ae 8880 pbseqlib_5.3.4+dfsg-3_arm64.buildinfo Checksums-Sha256: 7126cc69cf09c119efa8b9000194d0b5101a17955a4520c8c50e132b7e58b7e8 2042616 libblasr-dev_5.3.4+dfsg-3_arm64.deb 55171091dd4899838167b0eb7ce41d70ab6830b8edea555d8f518029a5da8073 8194468 libblasr5.3.4-dbgsym_5.3.4+dfsg-3_arm64.deb 920008c859398a4f5dacff2011fab88c441a543d81022a516f722cab24b9ea28 1038296 libblasr5.3.4_5.3.4+dfsg-3_arm64.deb 3d3df61d7dea6843b8ea167dbb4fe343f86005ccd5aaf0751493aa1b8b2e869e 40976 libpbdata-dev_5.3.4+dfsg-3_arm64.deb 404abeca3d56aba19dd9c0f1b8db4ef764879f0c7bd8048797fd2b8bab492b9b 47456 libpbihdf-dev_5.3.4+dfsg-3_arm64.deb ba075e85b3fcbcace0e152d3750ae15dc37c46619d12a76355b4d44e66048dfb 5220 libpbseq-dev_5.3.4+dfsg-3_arm64.deb 7c1a4ff288364be804065356d118971a09fc6256ce53b655e1c5bd59b12a38f7 5200 libpbseq_5.3.4+dfsg-3_arm64.deb 6ac044619f7b6b05de6377209470ec6342a56e4e4453b13004474d5a1d6734d5 8880 pbseqlib_5.3.4+dfsg-3_arm64.buildinfo Files: ceb43660769dcd98f316dcc2c92282b7 2042616 libdevel optional libblasr-dev_5.3.4+dfsg-3_arm64.deb ae498ae02609c7fd4d0633e185e8d5d3 8194468 debug optional libblasr5.3.4-dbgsym_5.3.4+dfsg-3_arm64.deb e47918a8fc7b5ebd122dd65a50368a72 1038296 libs optional libblasr5.3.4_5.3.4+dfsg-3_arm64.deb 87e37f75eccaaad884f09ed1df0a0022 40976 libdevel optional libpbdata-dev_5.3.4+dfsg-3_arm64.deb f57a20096902ff8a0fab0c8e0fb476ed 47456 libdevel optional libpbihdf-dev_5.3.4+dfsg-3_arm64.deb 5be13994a83b0563624e9a68c6dc3378 5220 libdevel optional libpbseq-dev_5.3.4+dfsg-3_arm64.deb eee7a2402760b8884e3f041a65e4275a 5200 science optional libpbseq_5.3.4+dfsg-3_arm64.deb 0fd069243a48567333d2af2dfa13209f 8880 science optional pbseqlib_5.3.4+dfsg-3_arm64.buildinfo Sun Aug 22 20:46:41 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/pbseqlib_5.3.4+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/pbseqlib_5.3.4+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/pbseqlib_5.3.4+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/b1/pbseqlib_5.3.4+dfsg-3_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.Zpqd6PfdUS/b2/pbseqlib_5.3.4+dfsg-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 7.091s) 7.091s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.943s) 0.942s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Aug 22 20:48:20 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Aug 22 20:48:20 UTC 2021 I: pbseqlib from bullseye built successfully and reproducibly on arm64. Sun Aug 22 20:48:39 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Aug 22 20:48:39 UTC 2021 I: Submitting 12K b1/pbseqlib_5.3.4+dfsg-3_arm64.buildinfo.asc Sun Aug 22 20:48:43 UTC 2021 I: Submitting 12K b2/pbseqlib_5.3.4+dfsg-3_arm64.buildinfo.asc Sun Aug 22 20:48:44 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Aug 22 20:48:44 UTC 2021 I: Done submitting .buildinfo files. Sun Aug 22 20:48:44 UTC 2021 I: Removing signed pbseqlib_5.3.4+dfsg-3_arm64.buildinfo.asc files: removed './b1/pbseqlib_5.3.4+dfsg-3_arm64.buildinfo.asc' removed './b2/pbseqlib_5.3.4+dfsg-3_arm64.buildinfo.asc'