Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pbseqlib/pbseqlib_5.3.4+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pbseqlib-5.3.4+dfsg-3f_9hy1es/pbseqlib_5.3.4+dfsg-3_amd64.buildinfo Get source package info: pbseqlib=5.3.4+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/pbseqlib/5.3.4+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.1.11 autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-4 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 cmake=3.18.4-1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 d-shlibs=0.95 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debian-archive-keyring=2019.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 googletest=1.10.0.20201025-1 gpgv=2.2.20-1 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hdf5-helpers=1.10.6+repack-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libaec-dev=1.0.4-1 libaec0=1.0.4-1 libapt-pkg6.0=2.1.11 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.0-17 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblkid1=2.36-3+b2 libboost-dev=1.71.0.3 libboost1.71-dev=1.71.0-7+b1 libbrotli1=1.0.9-2+b1 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libcurl3-gnutls=7.72.0-1 libcurl4=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.0-17 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libgtest-dev=1.10.0.20201025-1 libhdf5-103-1=1.10.6+repack-2 libhdf5-cpp-103-1=1.10.6+repack-2 libhdf5-dev=1.10.6+repack-2 libhdf5-fortran-102=1.10.6+repack-2 libhdf5-hl-100=1.10.6+repack-2 libhdf5-hl-cpp-100=1.10.6+repack-2 libhdf5-hl-fortran-100=1.10.6+repack-2 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-4 libidn2-0=2.3.0-3 libisl22=0.22.1-1 libitm1=10.2.0-17 libjpeg-dev=1:2.0.5-1.1 libjpeg62-turbo=1:2.0.5-1.1 libjpeg62-turbo-dev=1:2.0.5-1.1 libjsoncpp1=1.7.4-3.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-17 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpbbam-dev=1.6.0+dfsg-2 libpbbam1.6.0=1.6.0+dfsg-2 libpbcopper-dev=1.8.0+dfsg-2 libpbcopper1.8.0=1.8.0+dfsg-2 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpython3-stdlib=3.8.6-1 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libquadmath0=10.2.0-17 libreadline8=8.1~rc2-2 librhash0=1.4.0-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsemanage-common=3.1-1 libsemanage1=3.1-1+b1 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libsqlite3-0=3.33.0-1 libssh2-1=1.8.0-2.1 libssl-dev=1.1.1h-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libsub-override-perl=0.09-2 libsystemd0=246.6-2 libsz2=1.0.4-1 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 meson=0.56.0-1 mime-support=3.66 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 ninja-build=1.10.1-1 passwd=1:4.8.1-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 pkg-config=0.29.2-1 po-debconf=1.0.21 procps=2:3.3.16-5 python3=3.8.6-1 python3-minimal=3.8.6-1 python3-pkg-resources=50.3.0-1 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 readline-common=8.1~rc2-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T150139Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d pbseqlib=5.3.4+dfsg-3 && mkdir -p /build/pbseqlib-sPRg0y && dpkg-source --no-check -x /*.dsc /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg && chown -R builduser:builduser /build/pbseqlib-sPRg0y" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605530860" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/pbseqlib-sPRg0y /tmp/pbseqlib-5.3.4+dfsg-3f_9hy1es bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.0mMHczgktp as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.0mMHczgktp Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (534 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4695 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T150139Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.0mMHczgktp Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages [11.5 MB] Fetched 34.3 MB in 34s (1010 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.0mMHczgktp I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d pbseqlib=5.3.4+dfsg-3 && mkdir -p /build/pbseqlib-sPRg0y && dpkg-source --no-check -x /*.dsc /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg && chown -R builduser:builduser /build/pbseqlib-sPRg0y"' exec /tmp/mmdebstrap.0mMHczgktp Reading package lists... NOTICE: 'pbseqlib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pbseqlib.git Please use: git clone https://salsa.debian.org/med-team/pbseqlib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 970 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbseqlib 5.3.4+dfsg-3 (dsc) [2448 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbseqlib 5.3.4+dfsg-3 (tar) [958 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbseqlib 5.3.4+dfsg-3 (diff) [9444 B] Fetched 970 kB in 1s (1263 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'pbseqlib_5.3.4+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting pbseqlib in /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg.orig.tar.xz dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hdf5-1.10.1-support.patch dpkg-source: info: applying hdf5-1.10.0-support.patch dpkg-source: info: applying meson.patch dpkg-source: info: applying static+shared_lib.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605530860" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.0mMHczgktp dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' dh_auto_clean find -name defines.mk -delete rm -f pbdata/libconfig.h make[1]: Leaving directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 0.56.0 Source dir: /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg Build dir: /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: libblasr Project version: 5.3.4 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial' C++ compiler for the host machine: c++ (gcc 10.2.0 "c++ (Debian 10.2.0-17) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial' Host machine cpu family: 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: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.71.0 (/usr/include) Run-time dependency pbbam found: YES 1.6.0 Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-2 Library rt found: YES WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.49.0': disabler arg in dependency. Run-time dependency HDF5 for cpp found: YES 1.10.6 Configuring LibBlasrConfig.h using configuration Program tools/check-formatting found: YES (/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/tools/check-formatting) WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.53.0': Fallback without variable name. Run-time dependency GTest found: YES 1.10.0 Build targets in project: 3 WARNING: Project specifies a minimum meson_version '>= 0.46.0' but uses features which were added in newer versions: * 0.49.0: {'disabler arg in dependency'} * 0.53.0: {'Fallback without variable name'} Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -a cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:82:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 82 | DEFINE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:83:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 83 | DEFINE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:84:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 84 | DEFINE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:85:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 85 | DEFINE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:86:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 86 | DEFINE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:87:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 87 | DEFINE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:88:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 88 | DEFINE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [2/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [3/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:67:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 67 | DEFINE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:68:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 68 | DEFINE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char*]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:69:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 69 | DEFINE_TYPED_CREATE_ARRAY(char *, H5::StrType(0, H5T_VARIABLE)) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:70:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 70 | DEFINE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:71:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 71 | DEFINE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:72:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 72 | DEFINE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:73:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 73 | DEFINE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string]’: ../hdf/BufferedHDFArray.cpp:79:86: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), varStrType, space, cparms); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [4/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFAlnGroupGroup.hpp:6, from ../hdf/HDFAlnGroupGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: ../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ ../hdf/HDFAlnGroupGroup.cpp:16:29: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: ../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ ../hdf/HDFAlnGroupGroup.cpp:18:25: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [5/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp ../hdf/HDFAttributable.cpp: In member function ‘int HDFAttributable::ContainsAttribute(const string&)’: ../hdf/HDFAttributable.cpp:48:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 48 | } catch (H5::Exception e) { | ^ [6/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:9:92: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 9 | attribute = object.createAttribute(atomName.c_str(), strType, H5::DataSpace(H5S_SCALAR)); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:20:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 20 | DEFINE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:21:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 21 | DEFINE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:22:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 22 | DEFINE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:23:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 23 | DEFINE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:24:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 24 | DEFINE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:25:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 25 | DEFINE_TYPED_CREATE_ATOM(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:26:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 26 | DEFINE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 52 | } catch (H5::Exception e) { | ^ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [7/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAlnInfoGroup.cpp:44:77: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [8/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp [9/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp [10/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp ../hdf/HDFData.cpp: In member function ‘int HDFData::BaseInitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:37:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 37 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/HDFData.cpp: In member function ‘int HDFData::InitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:52:59: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 52 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [11/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp ../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’: ../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 18 | group = fg.openGroup(groupName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFGroup.hpp:9, from ../hdf/HDFGroup.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ [12/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:23:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 23 | } catch (FileIException e) { | ^ ../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:34:75: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ ../hdf/HDFFile.cpp:35:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 35 | } catch (FileIException fileException) { | ^~~~~~~~~~~~~ [13/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp ../hdf/HDFBaseCallsWriter.cpp: In member function ‘virtual void HDFBaseCallsWriter::Close()’: ../hdf/HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 364 | } catch (H5::Exception e) { | ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFBaseCallsWriter.hpp:12, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFBaseCallsWriter.cpp:342:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: ../hdf/HDFBaseCallsWriter.cpp:350:35: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [14/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp [15/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp [16/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFCmpExperimentGroup.hpp:10, from ../hdf/HDFCmpExperimentGroup.cpp:1: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned char]’ ../hdf/HDFCmpExperimentGroup.cpp:36:69: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]’: ../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = char]’ ../hdf/HDFCmpExperimentGroup.cpp:199:72: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [17/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [18/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp ../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: ../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 44 | for (auto annotation : annotations) | ^~~~~~~~~~~ In file included from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFWriterBase.hpp:17, from ../hdf/HDFRegionsWriter.hpp:13, from ../hdf/HDFRegionsWriter.cpp:3: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [19/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp [20/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:26:67: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:29:67: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:33:75: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [21/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp ../hdf/HDFPulseCallsWriter.cpp: In member function ‘virtual void HDFPulseCallsWriter::Close()’: ../hdf/HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 513 | } catch (H5::Exception e) { | ^ In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFWriterBase.hpp:12, from ../hdf/HDFPulseCallsWriter.hpp:12, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFPulseCallsWriter.cpp:492:47: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: ../hdf/HDFPulseCallsWriter.cpp:497:39: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: ../hdf/HDFPulseCallsWriter.cpp:498:49: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [22/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../hdf/HDFRegionTableReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFRegionTableReader.cpp:31:54: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../hdf/HDFRegionTableReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [23/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [24/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFWriterBase.cpp:49:88: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [25/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp [26/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp [27/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWMetricsWriter.hpp:7, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: ../hdf/HDFZMWMetricsWriter.cpp:54:27: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFZMWMetricsWriter.cpp:55:30: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWMetricsWriter.hpp:8, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWMetricsWriter.hpp:6, from ../hdf/HDFZMWMetricsWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [28/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [29/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp [30/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [31/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from ../alignment/algorithms/alignment/ExtendAlign.hpp:6, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [32/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWWriter.hpp:11, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: ../hdf/HDFZMWWriter.cpp:149:26: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ ../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: ../hdf/HDFZMWWriter.cpp:151:28: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWWriter.hpp:12, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWWriter.hpp:10, from ../hdf/HDFZMWWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [33/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/10/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFBasReader.hpp:21, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of ‘void T_HDFBasReader::GetMinMaxHoleNumber(UInt&, UInt&) [with T_Sequence = FASTASequence; UInt = unsigned int]’: ../hdf/HDFUtils.cpp:41:55: required from here ../hdf/HDFBasReader.hpp:1233:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 1233 | assert(nReads >= 0); | ~~~~~~~^~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFUtils.cpp:39:38: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [34/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from ../alignment/algorithms/alignment/GuidedAlign.hpp:6, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [35/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp [36/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp [37/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp [38/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp [39/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp [40/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from ../alignment/algorithms/alignment/KBandAlign.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [41/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp [42/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp [43/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp [44/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp [45/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp [46/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp [47/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat 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libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp [50/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp [51/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp [52/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp [53/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 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libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp ../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: ../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); | ^~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/datastructures/alignment/Alignment.cpp:2: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ [55/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp [56/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial 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-Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp [64/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp [65/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp [66/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from ../alignment/format/CompareSequencesPrinter.hpp:4, from ../alignment/format/CompareSequencesPrinter.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [67/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp [68/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp [69/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o -c ../alignment/format/SAMPrinter.cpp [70/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o -MF libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o -c ../alignment/query/SequentialZmwGroupQuery.cpp [71/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -MF libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -c ../alignment/query/PbiFilterZmwGroupQuery.cpp [72/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o -MF libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o -c ../alignment/qvs/QualityValueProfile.cpp [73/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [74/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o -c ../alignment/simulator/ContextSample.cpp [75/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/10/cassert:44, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, from ../alignment/simulator/LengthHistogram.hpp:8, from ../alignment/simulator/LengthHistogram.cpp:1: ../alignment/simulator/CDFMap.hpp: In instantiation of ‘int CDFMap::SelectRandomValue(T_Data&) [with T_Data = int]’: ../alignment/simulator/LengthHistogram.cpp:27:94: required from here ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ [76/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp [77/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o -c ../alignment/simulator/ContextSet.cpp [78/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp [79/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::Initialize(bool, bool)’: ../alignment/files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 267 | } catch (std::exception e) { | ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:360:50: required from here ../hdf/HDFBasReader.hpp:602:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 602 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:401:50: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:516:50: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]’: ../alignment/files/ReaderAgglomerate.cpp:611:64: required from here ../hdf/HDFBasReader.hpp:691:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 691 | } catch (H5::DataSetIException e) { | ^ In file included from ../alignment/files/ReaderAgglomerate.hpp:9, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: ../alignment/files/ReaderAgglomerate.cpp:664:50: required from here ../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 270 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../alignment/files/ReaderAgglomerate.cpp:250:56: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)’: ../alignment/files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=] 624 | std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl; | ^~~~ ../alignment/files/ReaderAgglomerate.cpp:626:9: note: here 626 | case FileType::Fourbit: | ^~~~ ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::GetNext(CCSSequence&)’: ../alignment/files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=] 669 | std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl; | ^~~~ ../alignment/files/ReaderAgglomerate.cpp:671:9: note: here 671 | case FileType::Fourbit: | ^~~~ [80/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o -MF libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o.d -o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o -c ../alignment/tuples/BaseTuple.cpp [81/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp [82/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o -MF libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o.d -o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o -c ../alignment/tuples/TupleMetrics.cpp [83/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o -c ../alignment/utils/BlasrFileUtils.cpp [84/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o -c ../alignment/simulator/QualitySample.cpp [85/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o -c ../alignment/utils/LogUtils.cpp [86/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o -c ../alignment/utils/PhredUtils.cpp [87/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o -c ../alignment/statistics/LookupAnchorDistribution.cpp [88/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.cpp [89/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o -c ../alignment/utils/RangeUtils.cpp [90/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o -MF libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp [91/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp [92/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp [93/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -c ../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp [94/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o -MF libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o -c ../pbdata/loadpulses/MetricField.cpp [95/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp [96/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp [97/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o -c ../pbdata/reads/AcqParams.cpp [98/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o -MF libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp [99/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp [100/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp [101/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp [102/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp [103/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp [104/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o -c ../pbdata/reads/RegionAnnotation.cpp [105/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o -c ../pbdata/reads/BaseFile.cpp [106/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp [107/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { | ^~~~~~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::RegionAnnotationsOfType(RegionType) const’: ../pbdata/reads/RegionAnnotations.cpp:37:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 37 | for (auto ra : table_) | ^~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘RegionAnnotation RegionAnnotations::TheHQRegion() const’: ../pbdata/reads/RegionAnnotations.cpp:65:22: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 65 | return hqs_[0]; | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ In file included from ../pbdata/reads/RegionAnnotations.cpp:3: ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] 8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ | ^~~ ../pbdata/reads/RegionAnnotations.cpp:67:9: note: in expansion of macro ‘BLASR_THROW’ 67 | BLASR_THROW("Zmw has more than one HQRegion"); | ^~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this ‘else’ clause 66 | else | ^~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::AdapterIntervals() const’: ../pbdata/reads/RegionAnnotations.cpp:84:34: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 84 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::SubreadIntervals(DNALength, bool, bool) const’: ../pbdata/reads/RegionAnnotations.cpp:102:42: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 102 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp:121:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 121 | for (auto insert : inserts) { | ^~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [108/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp [109/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp [110/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp [111/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp [112/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp [113/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp [114/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp [115/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp [116/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp [117/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp [118/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp [119/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp [120/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o -c ../pbdata/sam/SAMAlignment.cpp [121/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o -c ../pbdata/sam/SAMKeywordValuePair.cpp [122/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o -c ../pbdata/utils/SMRTTitle.cpp [123/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o -c ../pbdata/utils/TimeUtils.cpp [124/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp [125/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o -MF libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o -c ../pbdata/ChangeListID.cpp [126/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp [127/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp In file included from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/FASTASequence.hpp: In instantiation of ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = FASTASequence; _Args = {FASTASequence}]’: /usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]’ /usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*]’ /usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]’ /usr/include/c++/10/bits/stl_uninitialized.h:347:2: required from ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator]’ /usr/include/c++/10/bits/vector.tcc:659:48: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ /usr/include/c++/10/bits/stl_vector.h:940:4: required from ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ ../pbdata/BlasrFASTAReader.cpp:441:26: required from here ../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] 19 | class FASTASequence : public DNASequence | ^~~~~~~~~~~~~ In file included from ../pbdata/FASTASequence.hpp:13, from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ 51 | DNASequence &operator=(const DNASequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/bits/alloc_traits.h:33, from /usr/include/c++/10/ext/alloc_traits.h:34, from /usr/include/c++/10/bits/basic_string.h:40, from /usr/include/c++/10/string:55, from ../pbdata/FASTAReader.hpp:5, from ../pbdata/BlasrFASTAReader.cpp:2: /usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [128/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp [129/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o -MF libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o -c ../pbdata/GFFFile.cpp [130/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp [131/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o -MF libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o -c ../pbdata/NucConversion.cpp [132/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o -c ../pbdata/MD5Utils.cpp [133/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp [134/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp [135/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [136/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [137/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp [138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp [139/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp In file included from ../pbdata/SMRTSequence.cpp:3: ../pbdata/SMRTSequence.cpp: In member function ‘float SMRTSequence::HQRegionSnr(char) const’: ../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros] 8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \ | ^~~ ../pbdata/SMRTSequence.cpp:329:9: note: in expansion of macro ‘BLASR_THROW’ 329 | BLASR_THROW("Base must be in A, C, G, T"); | ^~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this ‘else’ clause 328 | else | ^~~~ ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: ../pbdata/SMRTSequence.cpp:353:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 353 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:378:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 378 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ [140/187] c++ -o libblasr.so.5.3.4 libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.4 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now /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 [141/187] /usr/bin/meson --internal symbolextractor /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu libblasr.so.5.3.4 libblasr.so.5.3.4 libblasr.so.5.3.4.p/libblasr.so.5.3.4.symbols [142/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o [143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp In file included from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ ../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFBasReader_gtest.cpp:33:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp [149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp [151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp [152/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp [153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp [157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp [158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp [160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp [161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: ../hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp [164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp In file included from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 270 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ ../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFCCSReader.hpp:93:57: required from ‘int HDFCCSReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:39:5: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp [168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp [169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -c ../unittest/pbdata/reads/RegionTypeMap_gtest.cpp [171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp [172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp [173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp [174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp [175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp [177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const string&, const UInt&, DNALength, DNALength, const string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 66 | return smrt; | ^~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymerase_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:133:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:133:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletion_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:192:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:192:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletionNoSubstitution_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:246:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:246:54: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ^ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ [179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp [180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp [181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp [182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp [183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp [184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -c ../unittest/pbdata/DNASequence_gtest.cpp [187/187] c++ -o unittest/libblasr_unittest unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now -Wl,--start-group libblasr.so.5.3.4 /usr/lib/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 -lpthread /usr/lib/x86_64-linux-gnu/libgtest.a -Wl,--end-group '-Wl,-rpath,$ORIGIN/..' -Wl,-rpath-link,/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu/ debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' /usr/bin/make -k gtest make[2]: Entering directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' make[2]: *** No rule to make target 'gtest'. make[2]: Leaving directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' make[1]: [debian/rules:31: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a cd obj-x86_64-linux-gnu && DESTDIR=/build/pbseqlib-sPRg0y/pbseqlib-5.3.4\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing libblasr.so.5.3.4 to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing libblasr.a to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu/LibBlasrConfig.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/BufferedHDF2DArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/BufferedHDF2DArrayImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/BufferedHDFArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/BufferedHDFArrayImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/DatasetCollection.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/DatasetCollectionImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDF2DArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFAlnGroupGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFAlnGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFAlnInfoGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFAtom.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFAttributable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFBaseCallsWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFBasReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFBasWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFBaxWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCCSReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpData.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpExperimentGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpRefAlignmentGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpRootGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCmpSupportedFields.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFCommonFG.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFConfig.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFData.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFFileLogGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFMovieInfoGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFNewBasReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFPlsReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFPlsWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFPulseCallsWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFPulseDataFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFPulseWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFRefGroupGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFRefInfoGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFRegionsWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFRegionTableReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFRegionTableWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFScanDataReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFScanDataWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFSentinalFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFSMRTSequenceReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFWriteBuffer.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFWriterBase.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFZMWMetricsWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFZMWReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/hdf/HDFZMWWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/FragmentSort.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPColumn.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPFragment.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPSet.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AffineGuidedAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AffineKBandAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentFormats.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/BaseScoreFunction.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/ExtendAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/FullQVAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GraphPaper.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GraphPaperImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/GuidedAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/IDSScoreFunction.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/KBandAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/OneGapAlignment.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/QualityValueScoreFunction.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/ScoreMatrices.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SDPAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SDPAlignImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/StringToScoreMatrix.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SWAlign.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/alignment/SWAlignImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BasicEndpoint.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BasicEndpointImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BWTSearch.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/BWTSearchImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ClusterProbability.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/Coordinate.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/FindMaxInterval.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/GlobalChain.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/GlobalChainImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValue.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueWeightor.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISQValueWeightor.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISSizeWeightor.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/MapBySuffixArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/PrioritySearchTree.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ScoreAnchors.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/compare/CompareStrings.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/compare Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/DifferenceCovers.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/Karkkainen.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/LightweightSuffixArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/MultikeyQuicksort.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/algorithms/sorting/qsufsort.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/bwt/BWT.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/bwt/Occ.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/bwt/PackedHash.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/bwt/Pos.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignedPair.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentCandidate.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentContext.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentGapList.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/Alignment.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentMap.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/AlignmentStats.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/ByteAlignment.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpIndexedStringTable.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpReadGroupTable.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/CmpRefSeqTable.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/FilterCriteria.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/Path.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/SAMQVConversion.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/AnchorParameters.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/ClusterList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/MatchPos.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/datastructures/anchoring/WeightedInterval.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/files/BaseSequenceIO.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/files/CCSIterator.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/files/FragmentCCSIterator.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/files/ReaderAgglomerate.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/files/ReaderAgglomerateImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/BAMPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/BAMPrinterImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/CompareSequencesPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/CompareSequencesPrinterImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/IntervalPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/SAMHeaderPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/SAMPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/SAMPrinterImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/StickAlignmentPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/SummaryPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/VulgarPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/format/XMLPrinter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/ipc/SharedMemoryAllocator.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/ipc Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/query/PbiFilterZmwGroupQuery.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/query/SequentialZmwGroupQuery.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/qvs/QualityValueProfile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/CDFMap.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextOutputList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextSample.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/ContextSet.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/LengthHistogram.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSample.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSampleList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/OutputSampleListSet.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/simulator/QualitySample.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/AnchorDistributionTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/cdfs.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/LookupAnchorDistribution.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/pdfs.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/StatUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/StatUtilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/VarianceAccumulator.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/statistics/VarianceAccumulatorImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/suffixarray/LCPTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SharedSuffixArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/suffixarray/ssort.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SuffixArray.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/suffixarray/SuffixArrayTypes.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/BaseTuple.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/CompressedDNATuple.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/CountedTuple.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATuple.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATupleImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/DNATupleList.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/HashedTupleList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/HashedTupleListImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleCountTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleCountTableImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/tuple.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleList.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleListImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMask.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMatching.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMatchingImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleMetrics.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleOperations.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/tuples/TupleTranslations.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/FileOfFileNames.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/FileUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/LogUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/PhredUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/RangeUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/RegionUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/RegionUtilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/utils/SimpleXMLUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/alignment/MappingMetrics.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/alignment/CmpAlignment.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/alignment/CmpAlignmentImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/amos/AfgBasWriter.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/amos Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/loadpulses/MetricField.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/matrix/FlatMatrix.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/matrix/FlatMatrixImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/matrix/Matrix.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/matrix/MatrixImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/metagenome/FindRandomSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/metagenome/SequenceIndexDatabase.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/metagenome/TitleTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityTransform.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValue.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityTransform.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValue.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVector.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/AcqParams.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/BaseFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/BaseFileImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/HoleXY.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseBaseCommon.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/PulseFileImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/ReadInterval.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/ReadType.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionAnnotation.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionAnnotations.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionTable.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/RegionTypeMap.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/ScanData.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/reads/ZMWGroupEntry.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/saf/AlnGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/saf/AlnInfo.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/saf/MovieInfo.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/saf/RefGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/saf/RefInfo.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/AlignmentSet.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/AlignmentSetImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/CigarString.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/ReadGroup.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/ReferenceSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMAlignment.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMFlag.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMHeader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMKeywordValuePair.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMKeywordValuePairImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/sam/SAMReaderImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utils/BitUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utils/SMRTReadUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utils/SMRTTitle.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utils/TimeUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/CCSSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/ChangeListID.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/CommandLineParser.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/Compare4BitCompressed.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/CompressedDNASequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/CompressedSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/CompressedSequenceImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/defs.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/DNASequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/Enumerations.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/FASTAReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/FASTASequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/FASTQReader.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/FASTQSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/GFFFile.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/MD5Utils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/MD5UtilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/NucConversion.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/PacBioDefs.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/PackedDNASequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/PrettyException.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/ReverseCompressIndex.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/SeqUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/SeqUtilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/SMRTSequence.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/StringUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/Types.h to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/utilsImpl.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/pbdata/VectorUtils.hpp to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu/meson-private/libblasr.pc to /build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/build/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' dh_install -p libpbdata-dev usr/include/libblasr/pbdata usr/include/pbseq dh_install -p libpbihdf-dev usr/include/libblasr/hdf usr/include/pbseq dh_install -p libblasr-dev usr/include/libblasr/alignment usr/include/pbseq find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete find debian/*/usr/include/ -name "*.mk" -delete d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libhdf5_serial_cpp103-dev/libhdf5-dev/ \ --override s/libpbbam1.6.0-dev/libpbbam-dev/ \ --override s/libpbcopper1.8.0-dev/libpbcopper-dev/ \ --movedev debian/tmp/usr/include/libblasr usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/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/libblasr5.3.4/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/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so.5.3.4 debian/libblasr5.3.4/usr/lib/x86_64-linux-gnu PKGDEV=libblasr-dev PKGSHL=libblasr5.3.4 install -d -m 755 debian/libblasr-dev/usr/include mv debian/tmp/usr/include/libblasr debian/libblasr-dev/usr/include install -d -m 755 debian/libblasr-dev/usr/lib/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/pbseqlib-sPRg0y/pbseqlib-5.3.4+dfsg' dh_installdocs -a dh_installchangelogs -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package libblasr-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libblasr5.3.4-dbgsym' in '../libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libblasr5.3.4' in '../libblasr5.3.4_5.3.4+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../pbseqlib_5.3.4+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/pbseqlib-sPRg0y /tmp/pbseqlib-5.3.4+dfsg-3f_9hy1es I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.0mMHczgktp... I: success in 2898.6533 seconds md5: libblasr-dev_5.3.4+dfsg-3_amd64.deb: OK md5: libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb: OK md5: libblasr5.3.4_5.3.4+dfsg-3_amd64.deb: OK md5: libpbdata-dev_5.3.4+dfsg-3_amd64.deb: OK md5: libpbihdf-dev_5.3.4+dfsg-3_amd64.deb: OK md5: libpbseq-dev_5.3.4+dfsg-3_amd64.deb: OK md5: libpbseq_5.3.4+dfsg-3_amd64.deb: OK sha1: libblasr-dev_5.3.4+dfsg-3_amd64.deb: OK sha1: libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb: OK sha1: libblasr5.3.4_5.3.4+dfsg-3_amd64.deb: OK sha1: libpbdata-dev_5.3.4+dfsg-3_amd64.deb: OK sha1: libpbihdf-dev_5.3.4+dfsg-3_amd64.deb: OK sha1: libpbseq-dev_5.3.4+dfsg-3_amd64.deb: OK sha1: libpbseq_5.3.4+dfsg-3_amd64.deb: OK sha256: libblasr-dev_5.3.4+dfsg-3_amd64.deb: OK sha256: libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb: OK sha256: libblasr5.3.4_5.3.4+dfsg-3_amd64.deb: OK sha256: libpbdata-dev_5.3.4+dfsg-3_amd64.deb: OK sha256: libpbihdf-dev_5.3.4+dfsg-3_amd64.deb: OK sha256: libpbseq-dev_5.3.4+dfsg-3_amd64.deb: OK sha256: libpbseq_5.3.4+dfsg-3_amd64.deb: OK Checksums: OK