I: pbuilder: network access will be disabled during build I: Current time: Wed May 8 02:08:31 +14 2024 I: pbuilder-time-stamp: 1715083711 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_5.3.5+dfsg-6.dsc] I: copying [./pbseqlib_5.3.5+dfsg.orig.tar.xz] I: copying [./pbseqlib_5.3.5+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Aug 22 18:48:33 2023 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pbseqlib_5.3.5+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting pbseqlib in pbseqlib-5.3.5+dfsg dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg-6.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 dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying pbbam_2.3.0 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 7 12:08 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=40ae403e935b4939a860d92aa31a2127 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2869409 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.knoPvjEv/pbuilderrc_YC6W --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.knoPvjEv/b2 --logfile b2/build.log pbseqlib_5.3.5+dfsg-6.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 7 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2869409/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: amd64 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 (>> 2.3.0), libpbcopper-dev (>> 2.2.0), 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 ... 19699 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 (>> 2.3.0); however: Package libpbbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbcopper-dev (>> 2.2.0); 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} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libgtest-dev{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam2.4.0{a} libpbcopper-dev{a} libpbcopper2.3.0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} ninja-build{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 110 newly installed, 0 to remove and 0 not upgraded. Need to get 70.1 MB of archives. After unpacking 398 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 54 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 googletest all 1.14.0-1 [512 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 75 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-5 [538 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.14.0-1+b1 [250 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [740 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b3 [819 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpbcopper-dev amd64 2.3.0+dfsg-2 [1071 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libpbbam-dev amd64 2.4.0+dfsg-1+b3 [88.4 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 ninja-build amd64 1.11.1-2 [142 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 meson all 1.4.0-2 [603 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Fetched 70.1 MB in 11s (6601 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Universal Time is now: Tue May 7 12:11:44 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up libssl-dev:amd64 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up d-shlibs (0.106) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240429-1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... 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Setting up libhdf5-dev (1.10.10+repack-3.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.38-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pbseqlib-5.3.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pbseqlib_5.3.5+dfsg-6_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.5+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' dh_auto_clean find -name defines.mk -delete rm -f pbdata/libconfig.h make[1]: Leaving directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.4.0 Source dir: /build/reproducible-path/pbseqlib-5.3.5+dfsg Build dir: /build/reproducible-path/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: libblasr Project version: 5.3.5 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Debian 13.2.0-24) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 Host machine cpu family: x86_64 Host machine cpu: x86_64 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: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr/include) Run-time dependency pbbam found: YES 2.4.0 Run-time dependency zlib found: YES 1.3 Run-time dependency htslib found: YES 1.19 Library rt found: YES Run-time dependency HDF5 for cpp found: YES 1.10.10 Configuring LibBlasrConfig.h using configuration Program tools/check-formatting found: YES (/build/reproducible-path/pbseqlib-5.3.5+dfsg/tools/check-formatting) Run-time dependency GTest found: YES 1.14.0 Build targets in project: 3 NOTICE: Future-deprecated features used: * 0.56.0: {'meson.build_root', 'meson.source_root'} libblasr 5.3.5 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j20 -v [1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp [2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/BufferedHDF2DArray.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp [4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp [5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.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: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:47, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5File.h:104:5: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 104 | 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:24:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 24 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:46: /usr/include/hdf5/serial/H5Group.h:62:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 62 | 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); | ^ [6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp [7/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [8/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.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:46, from ../hdf/HDFGroup.hpp:9, from ../hdf/HDFGroup.cpp:1: /usr/include/hdf5/serial/H5Group.h:62:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 62 | Group(const Group &original); | ^~~~~ [9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.5.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 std::string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.5.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 std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:26:33: 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:33, from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:29:33: 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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:33:39: 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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [11/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp [12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const std::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:33, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const std::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) | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const std::string&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::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)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp [14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp In file included from ../hdf/HDFAtom.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaxWriter.hpp:12, from ../hdf/HDFBaxWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionsWriter.hpp:9, from ../hdf/HDFRegionsWriter.cpp:3: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../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: ../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) | ^~~~~~~~~~~~~~~~ [16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFZMWReader.hpp:8, from ../hdf/HDFZMWReader.cpp:2: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAlnInfoGroup.cpp:44:23: 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:33, from ../hdf/BufferedHDF2DArray.hpp:8: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, from ../hdf/HDFRegionTableReader.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFRegionTableReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFRegionTableReader.cpp:31:31: 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:33, from ../hdf/HDFRegionTableReader.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFAtom.hpp:12, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFZMWReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:11: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFPulseDataFile.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp In file included from ../hdf/HDFAtom.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFPulseWriter.hpp:12, from ../hdf/HDFPulseWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp [22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp [23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp [24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp [25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp [26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDFZMWMetricsWriter.hpp:6, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWMetricsWriter.hpp:8: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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:33, from ../hdf/BufferedHDF2DArray.hpp:8: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp [28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp [29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFWriterBase.cpp:49:29: 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:33, from ../hdf/BufferedHDF2DArray.hpp:8: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp [31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp [32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp [33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp [34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp [35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp [36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp [37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp In file included from ../hdf/HDFAtom.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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:33, from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp [41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63, from ../alignment/algorithms/alignment/ExtendAlign.hpp:6: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDFZMWWriter.hpp:10, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFZMWWriter.hpp:12: ../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); | ^~~~~~~~~~~ ../hdf/HDFZMWWriter.hpp:55:10: note: by ‘HDFZMWWriter::WriteOneZmw’ 55 | bool WriteOneZmw(const SMRTSequence& read); | ^~~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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:33, from ../hdf/BufferedHDF2DArray.hpp:8: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp [44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp [45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp [46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63, from ../alignment/algorithms/alignment/KBandAlign.hpp:7: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp [48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp [49/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [50/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp [51/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from /usr/include/c++/13/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: ../hdf/HDFBasReader.hpp: In instantiation of ‘void T_HDFBasReader::GetMinMaxHoleNumber(UInt&, UInt&) [with T_Sequence = FASTASequence; UInt = unsigned int]’: ../hdf/HDFUtils.cpp:41:38: 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: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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:39:29: 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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [52/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp [53/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp [54/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp In file included from ../hdf/HDFAtom.hpp:12, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFPulseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [55/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp [56/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp [57/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp [58/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp [59/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp [60/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp [61/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp [62/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.5.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); | ^~~~~~~~ [63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp [64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -c ../alignment/tuples/BaseTuple.cpp [65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -c ../alignment/tuples/TupleMetrics.cpp [66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/13/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:27:87: 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); | ~~~~~~~~~~~^~~~ [67/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp [68/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp [69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp [70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp [71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_utils_LogUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o -c ../alignment/utils/LogUtils.cpp [72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1286:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: 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: ../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); | ^~~~~~~~ ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../alignment/format/CompareSequencesPrinter.hpp:4: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [73/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o -c ../alignment/utils/BlasrFileUtils.cpp [74/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_utils_PhredUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o -c ../alignment/utils/PhredUtils.cpp [75/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -c ../alignment/datastructures/alignment/FilterCriteria.cpp [76/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp [77/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp [78/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_simulator_QualitySample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o -c ../alignment/simulator/QualitySample.cpp [101/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp [102/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_simulator_ContextSet.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o -c ../alignment/simulator/ContextSet.cpp [103/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp [104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp [105/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -c ../alignment/query/PbiFilterZmwGroupQuery.cpp [106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp [107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp [108/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp [109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp [110/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.5.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_) | ^~~~~~ ../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]; | ^ ../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::AdapterIntervals() const’: ../pbdata/reads/RegionAnnotations.cpp:85:34: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 85 | for (auto adapter : Adapters()) { | ^ ../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:103:42: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 103 | for (auto adapter : Adapters()) { | ^ ../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:122:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 122 | for (auto insert : inserts) { | ^~~~~~~ ../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) | ^~~~~~~~~~~~~~~~ [111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -c ../pbdata/sam/SAMKeywordValuePair.cpp [112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -c ../pbdata/sam/SAMAlignment.cpp [113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp [114/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_BaseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o -c ../pbdata/reads/BaseFile.cpp [115/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_NucConversion.cpp.o -MF libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o -c ../pbdata/NucConversion.cpp [116/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp [117/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o -c ../pbdata/utils/SMRTTitle.cpp [118/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_ChangeListID.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o -c ../pbdata/ChangeListID.cpp [119/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_utils_TimeUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o -c ../pbdata/utils/TimeUtils.cpp [120/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_MD5Utils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o -c ../pbdata/MD5Utils.cpp [121/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp [122/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp [123/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp [124/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_GFFFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o -c ../pbdata/GFFFile.cpp [125/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_reads_PulseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp [126/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp [127/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp [128/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included 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: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [129/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp [130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.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::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_uninitialized.h:1077:26: required from ‘void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = FASTASequence; _Up = FASTASequence; _Allocator = allocator]’ /usr/include/c++/13/bits/stl_uninitialized.h:1105:26: required from ‘_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ /usr/include/c++/13/bits/stl_uninitialized.h:1147:33: required from ‘_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ /usr/include/c++/13/bits/stl_vector.h:509:26: required from ‘static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = FASTASequence; _Alloc = std::allocator; pointer = FASTASequence*; _Tp_alloc_type = std::vector::_Tp_alloc_type]’ /usr/include/c++/13/bits/vector.tcc:676:16: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ /usr/include/c++/13/bits/stl_vector.h:1016:4: required from ‘void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ ../pbdata/BlasrFASTAReader.cpp:441:21: 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: ../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/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from ../pbdata/FASTAReader.hpp:5: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp [133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp [134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp [135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp [136/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [137/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFRegionTableReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFRegionTableReader.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [138/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: ../pbdata/SMRTSequence.cpp:356:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 356 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:210:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 210 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:381:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 381 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:210:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 210 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ [139/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [141/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFRegionTableReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFRegionTableReader.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [145/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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:250:47: 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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFRegionTableReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFRegionTableReader.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [149/187] c++ -o libblasr.so.5.3.5 libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,-soname,libblasr.so.5.3.5 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath-link,/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--start-group /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [151/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o [152/187] /usr/bin/meson --internal symbolextractor /build/reproducible-path/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu libblasr.so.5.3.5 libblasr.so.5.3.5 libblasr.so.5.3.5.p/libblasr.so.5.3.5.symbols [153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFRegionTableReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFRegionTableReader.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFZMWReader.hpp:8, from ../unittest/hdf/HDFZMWReader_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../unittest/hdf/HDF2DArray_gtest.cpp:24: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp:28: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFPlsReader.hpp:9: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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 std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:124:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:125:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:126:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:127:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:128:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:137:1: required from here ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::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:33, from ../hdf/HDFData.hpp:6: /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::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()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:31:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 31 | Attribute(const Attribute &original); | ^~~~~~~~~ [184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 std::string&, const UInt&, DNALength, DNALength, const std::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:133:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../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++/13/vector:66, from /usr/include/gtest/gtest.h:62, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:133:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletion_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:192:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:192:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletionNoSubstitution_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:246:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:246:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:678:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 678 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 '-Wl,-rpath,$ORIGIN/..:/usr/lib/x86_64-linux-gnu/hdf5/serial' -Wl,-rpath-link,/build/reproducible-path/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/ -Wl,-rpath-link,/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--start-group libblasr.so.5.3.5 /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' /usr/bin/make -k gtest make[2]: Entering directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' make[2]: *** No rule to make target 'gtest'. make[2]: Leaving directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' make[1]: [debian/rules:30: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/build/reproducible-path/pbseqlib-5.3.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && DESTDIR=/build/reproducible-path/pbseqlib-5.3.5\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing libblasr.so.5.3.5 to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing libblasr.a to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/LibBlasrConfig.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/BufferedHDF2DArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/BufferedHDF2DArrayImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/BufferedHDFArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/BufferedHDFArrayImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/DatasetCollection.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/DatasetCollectionImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDF2DArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFAlnGroupGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFAlnGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFAlnInfoGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFAtom.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFAttributable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFBaseCallsWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFBasReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFBasWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFBaxWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCCSReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpData.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpExperimentGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpRefAlignmentGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpRootGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCmpSupportedFields.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFCommonFG.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFConfig.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFData.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFFileLogGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFMovieInfoGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFNewBasReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFPlsReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFPlsWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFPulseCallsWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFPulseDataFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFPulseWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFRefGroupGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFRefInfoGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFRegionsWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFRegionTableReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFRegionTableWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFScanDataReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFScanDataWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFSentinalFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFSMRTSequenceReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFWriteBuffer.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFWriterBase.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFZMWMetricsWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFZMWReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/hdf/HDFZMWWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/FragmentSort.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPColumn.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPFragment.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPSet.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AffineGuidedAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AffineKBandAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentFormats.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/BaseScoreFunction.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/ExtendAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/FullQVAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GraphPaper.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GraphPaperImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GuidedAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/IDSScoreFunction.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/KBandAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/OneGapAlignment.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/QualityValueScoreFunction.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/ScoreMatrices.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SDPAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SDPAlignImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/StringToScoreMatrix.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SWAlign.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SWAlignImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BasicEndpoint.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BasicEndpointImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BWTSearch.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BWTSearchImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ClusterProbability.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/Coordinate.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/FindMaxInterval.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/GlobalChain.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/GlobalChainImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValue.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueWeightor.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISQValueWeightor.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISSizeWeightor.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/MapBySuffixArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/PrioritySearchTree.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ScoreAnchors.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/compare/CompareStrings.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/compare Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/DifferenceCovers.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/Karkkainen.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/LightweightSuffixArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/MultikeyQuicksort.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/qsufsort.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/bwt/BWT.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/bwt/Occ.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/bwt/PackedHash.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/bwt/Pos.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignedPair.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentCandidate.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentContext.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentGapList.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/Alignment.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentMap.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentStats.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/ByteAlignment.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpIndexedStringTable.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpReadGroupTable.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpRefSeqTable.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/FilterCriteria.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/Path.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/SAMQVConversion.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/AnchorParameters.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/ClusterList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/MatchPos.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/WeightedInterval.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/files/BaseSequenceIO.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/files/CCSIterator.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/files/FragmentCCSIterator.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/files/ReaderAgglomerate.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/files/ReaderAgglomerateImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/BAMPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/BAMPrinterImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/CompareSequencesPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/CompareSequencesPrinterImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/IntervalPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/SAMHeaderPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/SAMPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/SAMPrinterImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/StickAlignmentPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/SummaryPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/VulgarPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/format/XMLPrinter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/ipc/SharedMemoryAllocator.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/ipc Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/query/PbiFilterZmwGroupQuery.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/query/SequentialZmwGroupQuery.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/qvs/QualityValueProfile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/CDFMap.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextOutputList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextSample.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextSet.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/LengthHistogram.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSample.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSampleList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSampleListSet.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/simulator/QualitySample.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/AnchorDistributionTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/cdfs.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/LookupAnchorDistribution.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/pdfs.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/StatUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/StatUtilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/VarianceAccumulator.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/statistics/VarianceAccumulatorImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/suffixarray/LCPTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SharedSuffixArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/suffixarray/ssort.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SuffixArray.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SuffixArrayTypes.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/BaseTuple.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/CompressedDNATuple.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/CountedTuple.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATuple.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATupleImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATupleList.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/HashedTupleList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/HashedTupleListImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleCountTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleCountTableImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/tuple.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleList.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleListImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMask.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMatching.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMatchingImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMetrics.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleOperations.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleTranslations.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/FileOfFileNames.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/FileUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/LogUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/PhredUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/RangeUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/RegionUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/RegionUtilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/utils/SimpleXMLUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/alignment/MappingMetrics.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/alignment/CmpAlignment.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/alignment/CmpAlignmentImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/amos/AfgBasWriter.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/amos Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/loadpulses/MetricField.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/matrix/FlatMatrix.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/matrix/FlatMatrixImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/matrix/Matrix.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/matrix/MatrixImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/metagenome/FindRandomSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/metagenome/SequenceIndexDatabase.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/metagenome/TitleTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityTransform.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValue.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityTransform.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValue.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/AcqParams.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/BaseFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/BaseFileImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/HoleXY.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseBaseCommon.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseFileImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/ReadInterval.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/ReadType.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionAnnotation.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionAnnotations.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionTable.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionTypeMap.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/ScanData.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/reads/ZMWGroupEntry.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/saf/AlnGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/saf/AlnInfo.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/saf/MovieInfo.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/saf/RefGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/saf/RefInfo.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/AlignmentSet.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/AlignmentSetImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/CigarString.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/ReadGroup.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/ReferenceSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMAlignment.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMFlag.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMHeader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMKeywordValuePair.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMKeywordValuePairImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMReaderImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utils/BitUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utils/SMRTReadUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utils/SMRTTitle.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utils/TimeUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/CCSSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/ChangeListID.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/CommandLineParser.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/Compare4BitCompressed.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/CompressedDNASequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/CompressedSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/CompressedSequenceImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/defs.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/DNASequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/Enumerations.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/FASTAReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/FASTASequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/FASTQReader.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/FASTQSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/GFFFile.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/MD5Utils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/MD5UtilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/NucConversion.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/PacBioDefs.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/PackedDNASequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/PrettyException.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/ReverseCompressIndex.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/SeqUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/SeqUtilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/SMRTSequence.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/StringUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/Types.h to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/utilsImpl.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/pbdata/VectorUtils.hpp to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/reproducible-path/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/meson-private/libblasr.pc to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig Installing symlink pointing to libblasr.so.5.3.5 to /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/pbseqlib-5.3.5+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/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libblasr5.3.5/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.a debian/libblasr-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so debian/libblasr-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so.5.3.5 debian/libblasr5.3.5/usr/lib/x86_64-linux-gnu PKGDEV=libblasr-dev PKGSHL=libblasr5.3.5 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/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libblasr-dev/usr/lib/x86_64-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/reproducible-path/pbseqlib-5.3.5+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 dh_md5sums dh_builddeb dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-6_amd64.deb'. dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbseqlib_5.3.5+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../pbseqlib_5.3.5+dfsg-6_amd64.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: user script /srv/workspace/pbuilder/2869409/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2869409/tmp/hooks/B01_cleanup finished 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/2869409 and its subdirectories I: Current time: Wed May 8 02:16:30 +14 2024 I: pbuilder-time-stamp: 1715084190