Build log for pbseqlib (5.3.5+dfsg-2) on armhf

pbseqlib → 5.3.5+dfsg-2 → armhf → 2021-10-14 14:34:59

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01

+==============================================================================+
| pbseqlib 5.3.5+dfsg-2 (armhf)                Thu, 14 Oct 2021 14:15:58 +0000 |
+==============================================================================+

Package: pbseqlib
Version: 5.3.5+dfsg-2
Source Version: 5.3.5+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-d65210ad-d068-473c-ad41-00db481e582a' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 25s (1015 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

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 985 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main pbseqlib 5.3.5+dfsg-2 (dsc) [2428 B]
Get:2 http://172.17.0.1/private bookworm-staging/main pbseqlib 5.3.5+dfsg-2 (tar) [973 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main pbseqlib 5.3.5+dfsg-2 (diff) [9444 B]
Fetched 985 kB in 0s (5269 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-xPhzEb/pbseqlib-5.3.5+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-xPhzEb' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-7js3fm/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-7js3fm/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7js3fm/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2789 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-7js3fm/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 34 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libpbcopper-dev, libhts-dev
Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libpbcopper-dev, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-7js3fm/apt_archive/sbuild-build-depends-pbseqlib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-pbseqlib-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Sources [570 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Packages [650 B]
Fetched 2553 B in 1s (3237 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-7js3fm/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...

Install pbseqlib build dependencies (apt-based resolver)
--------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
  d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file
  gcc-11-base gettext gettext-base googletest groff-base hdf5-helpers
  intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasan6
  libatomic1 libboost-dev libboost1.74-dev libbrotli1 libcc1-0 libcurl3-gnutls
  libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0
  libelf1 libexpat1 libffi8 libfile-stripnondeterminism-perl libgcc-s1
  libgfortran5 libglib2.0-0 libgomp1 libgtest-dev libhdf5-103-1
  libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100
  libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2
  libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp24
  liblzma-dev libmagic-mgc libmagic1 libmpdec3 libncurses6 libnghttp2-14
  libpbbam-dev libpbbam1.0.6 libpbcopper-dev libpbcopper1.3.0 libpipeline1
  libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal
  libpython3.9-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev
  libstdc++6 libsub-override-perl libsz2 libtool libubsan1 libuchardet0 libuv1
  libxml2 m4 man-db media-types meson ninja-build pkg-config po-debconf procps
  python3 python3-distutils python3-lib2to3 python3-minimal
  python3-pkg-resources python3.9 python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.74-doc
  libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
  libboost-context1.74-dev libboost-contract1.74-dev
  libboost-coroutine1.74-dev libboost-date-time1.74-dev
  libboost-exception1.74-dev libboost-fiber1.74-dev
  libboost-filesystem1.74-dev libboost-graph1.74-dev
  libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
  libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
  libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
  libboost-program-options1.74-dev libboost-python1.74-dev
  libboost-random1.74-dev libboost-regex1.74-dev
  libboost-serialization1.74-dev libboost-stacktrace1.74-dev
  libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
  libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
  libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
  libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
  librtmp-dev libssh2-1-dev libhdf5-doc liblzma-doc libssl-doc libtool-doc
  gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools
  python3.9-venv python3.9-doc binfmt-support
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs libgpm2 publicsuffix libltdl-dev
  libmail-sendmail-perl psmisc
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
  d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
  gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev
  libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.74-dev
  libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libelf1 libexpat1 libffi8
  libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgtest-dev
  libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
  libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
  libhtscodecs2 libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjsoncpp24 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libncurses6
  libnghttp2-14 libpbbam-dev libpbbam1.0.6 libpbcopper-dev libpbcopper1.3.0
  libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal
  libpython3.9-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev
  libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db
  media-types meson ninja-build pkg-config po-debconf procps python3
  python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources
  python3.9 python3.9-minimal sbuild-build-depends-pbseqlib-dummy
  sensible-utils zlib1g-dev
The following packages will be upgraded:
  gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6
  libubsan1
8 upgraded, 99 newly installed, 0 to remove and 26 not upgraded.
Need to get 59.5 MB of archives.
After this operation, 314 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7js3fm/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-8+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-8+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-8+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-8+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-8+rpi1 [36.1 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-8+rpi1 [37.8 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-8+rpi1 [8196 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-8+rpi1 [466 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-5 [67.4 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf d-shlibs all 0.100 [18.1 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf googletest all 1.11.0-2 [535 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-1 [42.7 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.8-1 [40.4 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-8+rpi1 [235 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libgtest-dev armhf 1.11.0-2 [1405 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-1 [1232 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.7+repack-1 [132 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.7+repack-1 [96.7 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-1 [81.8 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.7+repack-1 [53.5 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.7+repack-1 [39.8 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-4 [240 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.0.6-4 [67.8 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-1 [2195 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libpbcopper1.3.0 armhf 1.3.0+dfsg-3 [277 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libpbbam1.0.6 armhf 1.0.6+dfsg-2+rpi1 [565 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libssl-dev armhf 1.1.1l-1 [1581 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf libpbbam-dev armhf 1.0.6+dfsg-2+rpi1 [86.1 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libpbcopper-dev armhf 1.3.0+dfsg-3 [149 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf ninja-build armhf 1.10.1-1 [92.5 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf python3-pkg-resources all 52.0.0-4 [190 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf meson all 0.59.2-1 [496 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Setting up libhtscodecs2:armhf (1.1.1-3) ...
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
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Setting up libjpeg-dev:armhf (1:2.0.6-4) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libpbcopper-dev (1.3.0+dfsg-3) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up libhdf5-103-1:armhf (1.10.7+repack-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up procps (2:3.3.17-5) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.7+repack-1) ...
Setting up libcurl4:armhf (7.74.0-1.3) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up libhdf5-hl-100:armhf (1.10.7+repack-1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up python3 (3.9.2-3) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
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Setting up libpbbam1.0.6:armhf (1.0.6+dfsg-2+rpi1) ...
Setting up libhdf5-fortran-102:armhf (1.10.7+repack-1) ...
Setting up cmake (3.18.4-2+rpi1) ...
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Setting up libpbbam-dev (1.0.6+dfsg-2+rpi1) ...
Setting up python3-lib2to3 (3.9.7-1) ...
Setting up python3-pkg-resources (52.0.0-4) ...
Setting up python3-distutils (3.9.7-1) ...
Setting up meson (0.59.2-1) ...
Setting up debhelper (13.5.2) ...
Setting up libhdf5-dev (1.10.7+repack-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up sbuild-build-depends-pbseqlib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-8+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 cmake_3.18.4-2+rpi1 cmake-data_3.18.4-2+rpi1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 d-shlibs_0.100 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-8+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 googletest_1.11.0-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hdf5-helpers_1.10.7+repack-1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_11.2.0-8+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-8+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-8+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-8+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran5_11.2.0-8+rpi1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-8+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libgtest-dev_1.11.0-2 libhdf5-103-1_1.10.7+repack-1 libhdf5-cpp-103-1_1.10.7+repack-1 libhdf5-dev_1.10.7+repack-1 libhdf5-fortran-102_1.10.7+repack-1 libhdf5-hl-100_1.10.7+repack-1 libhdf5-hl-cpp-100_1.10.7+repack-1 libhdf5-hl-fortran-100_1.10.7+repack-1 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjpeg-dev_1:2.0.6-4 libjpeg62-turbo_1:2.0.6-4 libjpeg62-turbo-dev_1:2.0.6-4 libjsoncpp24_1.9.4-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpbbam-dev_1.0.6+dfsg-2+rpi1 libpbbam1.0.6_1.0.6+dfsg-2+rpi1 libpbcopper-dev_1.3.0+dfsg-3 libpbcopper1.3.0_1.3.0+dfsg-3 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl-dev_1.1.1l-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-8+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-8+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libuv1_1.42.0-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 meson_0.59.2-1 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ninja-build_1.10.1-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3-pkg-resources_52.0.0-4 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.BE5XWTyf/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct  8 13:49:12 2021 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.5+dfsg-2.dsc
dpkg-source: info: extracting pbseqlib in /<<BUILDDIR>>/pbseqlib-5.3.5+dfsg
dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg-2.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

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-d65210ad-d068-473c-ad41-00db481e582a
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.5+dfsg-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.5+dfsg'
dh_auto_clean
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.5+dfsg'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
	cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf
The Meson build system
Version: 0.59.2
Source dir: /<<BUILDDIR>>/pbseqlib-5.3.5+dfsg
Build dir: /<<BUILDDIR>>/pbseqlib-5.3.5+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: libblasr
Project version: 5.3.5
C++ compiler for the host machine: c++ (gcc 10.3.0 "c++ (Raspbian 10.3.0-9+rpi1) 10.3.0")
C++ linker for the host machine: c++ ld.bfd 2.37
Host machine cpu family: arm
Host machine cpu: armv7l
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-unused-variable: YES 
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES 
Found pkg-config: /usr/bin/pkg-config (0.29.2)
Run-time dependency Boost found: YES 1.74.0 (/usr/include)
Run-time dependency pbbam found: YES 1.0.6
Run-time dependency zlib found: YES 1.2.11
Run-time dependency htslib found: YES 1.13+ds
Library rt found: YES
Run-time dependency HDF5 for cpp found: YES 1.10.7
Configuring LibBlasrConfig.h using configuration
Program tools/check-formatting found: YES (/<<BUILDDIR>>/pbseqlib-5.3.5+dfsg/tools/check-formatting)
Run-time dependency GTest found: YES 1.11.0
Build targets in project: 3

Option buildtype is: plain [default: release]
Found ninja-1.10.1 at /usr/bin/ninja
   dh_auto_build -a
	cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp
../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray<T>::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<T>::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<T>::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<T>::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<T>::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<T>::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<T>::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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp
[3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp
../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray<T>::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<T>::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<T>::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<T>::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<T>::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<T>::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<T>::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<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string<char>]’:
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp
[5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp
[6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp
../hdf/HDFAtom.cpp: In member function ‘void HDFAtom<T>::Create(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = long long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::vector<int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, std::vector<int>&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp
In file included from ../hdf/HDFAlnInfoGroup.hpp:10,
                 from ../hdf/HDFAlnInfoGroup.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp
[9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp
../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);
      |         ^~~~~~~
[10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp
[11/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp
../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’:
../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy]
   34 |             hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList);
      |                                                                           ^
In file included from /usr/include/hdf5/serial/H5Cpp.h: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);
      |                                                                           ^
[12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp
../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’:
../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy]
   18 |         group = fg.openGroup(groupName.c_str());
      |                                               ^
In file included from /usr/include/hdf5/serial/H5Cpp.h: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);
      |         ^~~~~
[13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp
In file included from ../hdf/HDFBaseCallsWriter.hpp:11,
                 from ../hdf/HDFBaseCallsWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp
[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp
[16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp
[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp
[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp
In file included from ../hdf/HDFScanDataReader.hpp:8,
                 from ../hdf/HDFPulseDataFile.hpp:10,
                 from ../hdf/HDFPulseDataFile.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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);
      |         ^~~~~~~~~
[19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp
../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector<RegionAnnotation>&)’:
../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy]
   44 |     for (auto annotation : annotations)
      |                            ^~~~~~~~~~~
In file included from ../pbdata/reads/RegionTable.hpp:17,
                 from ../pbdata/SMRTSequence.hpp:14,
                 from ../hdf/HDFWriterBase.hpp:17,
                 from ../hdf/HDFRegionsWriter.hpp:13,
                 from ../hdf/HDFRegionsWriter.cpp:3:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’
  115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
      |                          ^~~~~~~~~~~~~~~~
[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp
In file included from ../hdf/HDFPulseCallsWriter.hpp:11,
                 from ../hdf/HDFPulseCallsWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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);
      |         ^~~~~~~~~
[21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp
In file included from ../hdf/HDFScanDataReader.hpp:8,
                 from ../hdf/HDFScanDataReader.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFScanDataReader.cpp:33:75:   required from here
../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy]
   33 |         attribute = object.openAttribute(attributeName.c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf5/serial/H5Cpp.h:34,
                 from ../hdf/HDFAtom.hpp:9,
                 from ../hdf/HDFScanDataReader.hpp:8,
                 from ../hdf/HDFScanDataReader.cpp:1:
/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’
   33 |         Attribute(const Attribute& original);
      |         ^~~~~~~~~
[22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp
In file included from ../hdf/HDFRegionTableReader.hpp:11,
                 from ../hdf/HDFRegionTableReader.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:45:26:   required from ‘int HDFAtom<T>::Initialize(HDFData&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp
In file included from ../hdf/HDFScanDataWriter.hpp:10,
                 from ../hdf/HDFScanDataWriter.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp
In file included from ../hdf/HDFWriterBase.hpp:13,
                 from ../hdf/HDFWriterBase.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom<T>::Create(H5::H5Object&, const string&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp
[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp
[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp
In file included from ../hdf/HDFWriterBase.hpp:13,
                 from ../hdf/HDFZMWMetricsWriter.hpp:8,
                 from ../hdf/HDFZMWMetricsWriter.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
                 from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9,
                 from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __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<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/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<blasr::CompSeqAlignment>; 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/arm-linux-gnueabihf/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:156:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
  156 |  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp
[30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
                 from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __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<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/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<blasr::CompSeqAlignment>; 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/arm-linux-gnueabihf/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:156:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
  156 |  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp
In file included from /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<T_Sequence>::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<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFBasReader.hpp:273:40:   required from ‘int T_HDFBasReader<T_Sequence>::InitializeForReadingBases() [with T_Sequence = FASTASequence]’
../hdf/HDFBasReader.hpp:323:13:   required from ‘int T_HDFBasReader<T_Sequence>::InitializeCommon() [with T_Sequence = FASTASequence]’
../hdf/HDFBasReader.hpp:518:13:   required from ‘int T_HDFBasReader<T_Sequence>::Initialize() [with T_Sequence = FASTASequence]’
../hdf/HDFBasReader.hpp:581:26:   required from ‘int T_HDFBasReader<T_Sequence>::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’
../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<T>::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’
../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);
      |         ^~~~~~~~~
[32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp
In file included from ../hdf/HDFWriterBase.hpp:13,
                 from ../hdf/HDFZMWWriter.hpp:12,
                 from ../hdf/HDFZMWWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26:   required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’
../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.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
                 from ../alignment/algorithms/alignment/KBandAlign.hpp:10,
                 from ../alignment/algorithms/alignment/ExtendAlign.hpp:9,
                 from ../alignment/algorithms/alignment/ExtendAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __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<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/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<blasr::CompSeqAlignment>; 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/arm-linux-gnueabihf/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:156:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
  156 |  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
                 from ../alignment/algorithms/alignment/GuidedAlign.hpp:11,
                 from ../alignment/algorithms/alignment/GuidedAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __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<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/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<blasr::CompSeqAlignment>; 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/arm-linux-gnueabihf/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:156:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
  156 |  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp
[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp
[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
                 from ../alignment/algorithms/alignment/KBandAlign.hpp:10,
                 from ../alignment/algorithms/alignment/KBandAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __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<std::allocator<_CharT> >::construct(std::allocator_traits<std::allocator<_CharT> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_CharT> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/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<blasr::CompSeqAlignment>; 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/arm-linux-gnueabihf/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:156:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
  156 |  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp
[39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp
[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp
[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp
[42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp
[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp
FAILED: libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o 
c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp
In file included from ../alignment/bwt/BWT.hpp:9,
                 from ../alignment/algorithms/anchoring/BWTSearch.hpp:6,
                 from ../alignment/algorithms/anchoring/BWTSearch.cpp:1:
../alignment/suffixarray/SuffixArray.hpp: In member function ‘void SuffixArray<T, Sigma, Compare, Tuple>::LarssonBuildSuffixArray(T*, SAIndexLength, Sigma&)’:
../alignment/suffixarray/SuffixArray.hpp:288:44: error: narrowing conversion of ‘4294967295’ from ‘unsigned int’ to ‘long int’ [-Wnarrowing]
  288 |         LarssonSuffixSort<SAIndex, UINT_MAX> sorter;
      |                                            ^
../alignment/suffixarray/SuffixArray.hpp:289:84: error: ‘sorter’ cannot be used as a function
  289 |         sorter(index, p, ((SAIndex)targetLength), ((SAIndex)maxVal + 1), (SAIndex)1);
      |                                                                                    ^
[44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp
[45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp
[46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.5+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.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:25: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2021-10-14T14:34:55Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 0
Build-Time: 301
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 789
Job: pbseqlib_5.3.5+dfsg-2
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1137
Source-Version: 5.3.5+dfsg-2
Space: 0
Status: failed
Version: 5.3.5+dfsg-2
--------------------------------------------------------------------------------
Finished at 2021-10-14T14:34:55Z
Build needed 00:00:00, 0k disc space
Raspbian Package Auto-Building

Build log for pbseqlib (5.3.5+dfsg-2) on armhf
