I: pbuilder: network access will be disabled during build
I: Current time: Mon Feb 17 06:57:17 +14 2025
I: pbuilder-time-stamp: 1739725037
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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-9.dsc]
I: copying [./pbseqlib_5.3.5+dfsg.orig.tar.xz]
I: copying [./pbseqlib_5.3.5+dfsg-9.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./pbseqlib_5.3.5+dfsg-9.dsc: unsupported subcommand
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-9.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
dpkg-source: info: applying gcc-14.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/56623/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 Feb 16 16:57 /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/56623/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/56623/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(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=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=0a257438b3204956b5b8a4590d644add
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=56623
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.fkyVPIeB/pbuilderrc_LmTm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fkyVPIeB/b2 --logfile b2/build.log pbseqlib_5.3.5+dfsg-9.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 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/56623/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 <pbuilder-maint@lists.alioth.debian.org>
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, pkgconf, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>> 2.3.0), libpbcopper-dev (>> 2.2.0), libhts-dev (>= 1.20+ds-2~)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19808 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 pkgconf; however:
Package pkgconf 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 (>= 1.20+ds-2~); 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} comerr-dev{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} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpbbam-dev{a} libpbbam2.4.0{a} libpbcopper-dev{a} libpbcopper2.3.0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} nettle-dev{a} ninja-build{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 153 newly installed, 0 to remove and 0 not upgraded.
Need to get 85.2 MB of archives. After unpacking 445 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.5-2 [2267 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 41 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.0+git20250209.89ed161+ds-1 [355 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.5-2 [12.0 MB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.109 [11.1 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 googletest all 1.15.2-1 [514 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.0+git20250209.89ed161+ds-1 [365 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.0+git20250209.89ed161+ds-1 [479 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libgtest-dev amd64 1.15.2-1 [259 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2+b2 [736 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b4 [835 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libpbcopper-dev amd64 2.3.0+dfsg-2+b2 [1072 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libpbbam-dev amd64 2.4.0+dfsg-1+b4 [88.4 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 ninja-build amd64 1.12.1-1 [142 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 meson all 1.7.0-1 [639 kB]
Fetched 85.2 MB in 9s (9685 kB/s)
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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'
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Setting up libboost-dev:amd64 (1.83.0.2+b2) ...
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Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ...
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Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
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Setting up intltool-debian (0.35.0+20060710.6) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up libcurl4t64:amd64 (8.12.0+git20250209.89ed161+ds-1) ...
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Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libhdf5-310:amd64 (1.14.5+repack-3) ...
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Setting up cmake (3.31.5-2) ...
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Setting up python3-setuptools (75.6.0-1) ...
Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b4) ...
Setting up meson (1.7.0-1) ...
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Setting up libcurl4-gnutls-dev:amd64 (8.12.0+git20250209.89ed161+ds-1) ...
Setting up libhdf5-dev (1.14.5+repack-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
Setting up libhts-dev:amd64 (1.21+ds-1) ...
Setting up libpbbam-dev:amd64 (2.4.0+dfsg-1+b4) ...
Processing triggers for libc-bin (2.40-6) ...
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/56623/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/56623/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-9_source.changes
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.5+dfsg-9
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
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: 1.7.0
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 14.2.0 "c++ (Debian 14.2.0-16) 14.2.0")
C++ linker for the host machine: c++ ld.bfd 2.44
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 1.3.1
Run-time dependency htslib found: YES 1.21
Library rt found: YES
Run-time dependency HDF5 for cpp found: YES 1.14.5
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 1.15.0
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
python.bytecompile: -1
sysconfdir : /etc
wrap_mode : nodownload
Found ninja-1.12.1 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_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:115:5: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’
115 | H5File(const H5File &original);
| ^~~~~~
[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_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
[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_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
[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_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
[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_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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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
[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/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
[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/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
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[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_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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<RegionAnnotation>&)’:
../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)
| ^~~~~~~~~~~~~~~~
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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/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
[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/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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[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_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
[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/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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/vector:63,
from ../alignment/algorithms/alignment/KBandAlign.hpp:7:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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
[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/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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43,
from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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
[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_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
[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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/vector:63,
from ../alignment/algorithms/alignment/ExtendAlign.hpp:6:
/usr/include/c++/14/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/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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43,
from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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
[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
In file included from ../alignment/algorithms/anchoring/FindMaxInterval.hpp:16,
from ../alignment/algorithms/anchoring/FindMaxInterval.cpp:1:
../alignment/statistics/VarianceAccumulator.hpp:14:27: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
14 | VarianceAccumulator<T>();
| ^
../alignment/statistics/VarianceAccumulator.hpp:14:27: note: remove the ‘< >’
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<RegionAnnotation>&)’ was hidden [-Woverloaded-virtual=]
43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector<RegionAnnotation>& regions);
| ^~~~~~~~~~~
../hdf/HDFZMWWriter.hpp:55:10: note: by ‘HDFZMWWriter::WriteOneZmw’
55 | bool WriteOneZmw(const SMRTSequence& read);
| ^~~~~~~~~~~
[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_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
[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_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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from ../alignment/algorithms/alignment/GuidedAlign.hpp:6:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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
[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_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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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_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
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
In file included from /usr/include/c++/14/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<T_Sequence>::GetMinMaxHoleNumber(UInt&, UInt&) [with T_Sequence = FASTASequence; UInt = unsigned int]’:
../hdf/HDFUtils.cpp:41:38: required from here
41 | basReader.GetMinMaxHoleNumber(minHole, maxHole);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
../hdf/HDFBasReader.hpp:1233:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits]
1233 | assert(nReads >= 0);
| ~~~~~~~^~~~
[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_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
[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_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
[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_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
[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_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
[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_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
[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_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);
| ^~~~~~~~
[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_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
[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_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
[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_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
[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_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
[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_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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1289 | __x);
| ~~~~
../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
112 | alignments.push_back(alignment);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ../alignment/format/CompareSequencesPrinter.hpp:4:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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++/14/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<T_Data>::SelectRandomValue(T_Data&) [with T_Data = int]’:
../alignment/simulator/LengthHistogram.cpp:27:87: required from here
27 | void LengthHistogram::GetRandomLength(int &length) { lengthHistogram.SelectRandomValue(length); }
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits]
37 | assert(cdf.size() >= 0);
| ~~~~~~~~~~~^~~~
[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_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
[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_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
[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_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
[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_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
[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_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
[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_query_SequentialZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -c ../alignment/query/SequentialZmwGroupQuery.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/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
[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_format_SAMPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o -c ../alignment/format/SAMPrinter.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 libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o -c ../alignment/utils/RangeUtils.cpp
[79/187] 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_qvs_QualityValueProfile.cpp.o -MF libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o -c ../alignment/qvs/QualityValueProfile.cpp
[80/187] 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_AcqParams.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o -c ../pbdata/reads/AcqParams.cpp
[81/187] 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_loadpulses_MovieAlnIndexLookupTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -c ../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp
[82/187] 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
[83/187] 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_HoleXY.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp
[84/187] 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_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
[85/187] 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_loadpulses_MetricField.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o -c ../pbdata/loadpulses/MetricField.cpp
[86/187] 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_qvs_BlasrQualityValue.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp
[87/187] 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_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp
[88/187] 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_MappingMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp
[89/187] 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_ContextSample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -c ../alignment/simulator/ContextSample.cpp
[90/187] 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_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp
[91/187] 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_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp
[92/187] 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_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp
[93/187] 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_LookupAnchorDistribution.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o -c ../alignment/statistics/LookupAnchorDistribution.cpp
[94/187] 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
[95/187] 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_ReadType.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp
[96/187] 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_AlnGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp
[97/187] 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
[98/187] 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_RefGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp
[99/187] 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
[100/187] 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
[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/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.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/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.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_reads_RegionAnnotation.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o -c ../pbdata/reads/RegionAnnotation.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/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
[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_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
[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_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
[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_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
[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_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
[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<RegionAnnotation>&, const std::vector<T_RegionType>&)’:
../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<RegionAnnotation> 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<ReadInterval> 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<ReadInterval> 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_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
[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_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
[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_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
[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_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
[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_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
[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_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
[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_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
[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_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
[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/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
[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_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
[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/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
[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_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
[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_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
[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/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
[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_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
[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_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
[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_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++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence; allocator_type = std::allocator<FASTASequence>]’
575 | __a.construct(__p, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_uninitialized.h:1075:26: required from ‘void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = FASTASequence; _Up = FASTASequence; _Allocator = allocator<FASTASequence>]’
1075 | __traits::construct(__alloc, __dest, std::move(*__orig));
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_uninitialized.h:1103:26: required from ‘_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator<FASTASequence>]’
1103 | std::__relocate_object_a(std::__addressof(*__cur),
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1104 | std::__addressof(*__first), __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_uninitialized.h:1145:33: required from ‘_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator<FASTASequence>]’
1145 | return std::__relocate_a_1(std::__niter_base(__first),
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1146 | std::__niter_base(__last),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
1147 | std::__niter_base(__result), __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/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<FASTASequence>; pointer = FASTASequence*; _Tp_alloc_type = std::vector<FASTASequence>::_Tp_alloc_type]’
509 | return std::__relocate_a(__first, __last, __result, __alloc);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/vector.tcc:868:18: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; size_type = long unsigned int]’
868 | _S_relocate(__old_start, __old_finish,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
869 | __new_start, _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_vector.h:1016:4: required from ‘void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; size_type = long unsigned int]’
1016 | _M_default_append(__new_size - size());
| ^~~~~~~~~~~~~~~~~
../pbdata/BlasrFASTAReader.cpp:441:21: required from here
441 | sequences.resize(nSeq);
| ~~~~~~~~~~~~~~~~^~~~~~
../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++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43,
from ../pbdata/FASTAReader.hpp:5:
/usr/include/c++/14/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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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_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
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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++ -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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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_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<SMRTSequence>&)’:
../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)
| ^~~~~~~~~~~~
[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_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
[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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[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_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
[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/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
[145/187] 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
[146/187] /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
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[149/187] 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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[151/187] 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
[152/187] 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
[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/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
[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_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
[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/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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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/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
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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_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
[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_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
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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/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
[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_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
[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_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp
[175/187] 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
[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/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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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/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<int>’:
../hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<unsigned char>’:
../hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short unsigned int>’:
../hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
| ^~
../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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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
[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_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
[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/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
[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/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
[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++/14/vector:66,
from /usr/include/gtest/gtest.h:61,
from ../unittest/pbdata/SMRTSequence_gtest.cpp:22:
/usr/include/c++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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++/14/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<SMRTSequence>; allocator_type = std::allocator<SMRTSequence>]’
678 | vector(initializer_list<value_type> __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 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-9_amd64.deb'.
dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-9_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../pbseqlib_5.3.5+dfsg-9_amd64.buildinfo
dpkg-genchanges --build=binary -O../pbseqlib_5.3.5+dfsg-9_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/56623/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/56623/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/56623 and its subdirectories
I: Current time: Mon Feb 17 07:02:48 +14 2025
I: pbuilder-time-stamp: 1739725368