pbseqlib →
5.3.4+dfsg-3 →
armhf → 2021-03-19 05:04:53
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| pbseqlib 5.3.4+dfsg-3 (armhf) Fri, 19 Mar 2021 04:57:47 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 5.3.4+dfsg-3
Source Version: 5.3.4+dfsg-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-44c22f35-3f56-4d08-b807-3fd79c889d70' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 12s (2078 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 970 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.4+dfsg-3 (dsc) [2448 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.4+dfsg-3 (tar) [958 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.4+dfsg-3 (diff) [9444 B]
Fetched 970 kB in 0s (2212 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-2A0WyC/pbseqlib-5.3.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-2A0WyC' 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-MVSjXf/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-MVSjXf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MVSjXf/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-MVSjXf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (7006 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libnss-nis libnss-nisplus libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 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-MVSjXf/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 (51.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12557 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 (>= 0.18.0+dfsg-1~), 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 (>= 0.18.0+dfsg-1~), libpbcopper-dev, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-MVSjXf/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-MVSjXf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Sources [589 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ Packages [670 B]
Fetched 2592 B in 1s (4999 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pbseqlib build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev 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
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
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-minimal python3-pkg-resources python3.9 python3.9-minimal 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 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
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
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-minimal python3-pkg-resources python3.9 python3.9-minimal
sbuild-build-depends-pbseqlib-dummy zlib1g-dev
0 upgraded, 93 newly installed, 0 to remove and 2 not upgraded.
Need to get 55.1 MB of archives.
After this operation, 312 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MVSjXf/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.2-1+rpi1 [791 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.2-1+rpi1 [1625 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.2-2 [38.2 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.2-1+rpi1 [1616 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.2-1+rpi1 [466 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.2-2 [21.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.2-2 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.17-4 [60.5 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.17-4 [476 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1.1 [304 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.1-1 [140 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.98 [17.9 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.4 [1049 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf googletest all 1.10.0.20201025-1.1 [629 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.6+repack-2 [40.0 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.1 [301 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.1 [375 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.7-2 [1183 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.10.0.20201025-1.1 [1388 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [128 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [93.0 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [78.1 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [49.8 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [36.9 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-2 [122 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-2 [240 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev armhf 1:2.0.6-2 [67.6 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.6+repack-2 [2167 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper1.3.0 armhf 1.3.0+dfsg-3 [277 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpbbam1.0.6 armhf 1.0.6+dfsg-2+rpi1 [565 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1j-1 [1576 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpbbam-dev armhf 1.0.6+dfsg-2+rpi1 [86.1 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper-dev armhf 1.3.0+dfsg-3 [149 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.10.1-1 [92.5 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 52.0.0-3 [189 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.56.2-1 [437 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 55.1 MB in 9s (5896 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12557 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../2-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../3-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../4-libpython3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../5-libexpat1_2.2.10-2_armhf.deb ...
Unpacking libexpat1:armhf (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../6-python3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.2-1+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13393 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-2_armhf.deb ...
Unpacking python3-minimal (3.9.2-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../2-libmpdec3_2.5.1-1+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-1+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../3-libpython3.9-stdlib_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../4-python3.9_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.2-1+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../5-libpython3-stdlib_3.9.2-2_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-2) ...
Setting up python3-minimal (3.9.2-2) ...
Selecting previously unselected package python3.
(Reading database ... 13790 files and directories currently installed.)
Preparing to unpack .../00-python3_3.9.2-2_armhf.deb ...
Unpacking python3 (3.9.2-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../01-libncurses6_6.2+20201114-2_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-2) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../02-libprocps8_2%3a3.3.17-4_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.17-4) ...
Selecting previously unselected package procps.
Preparing to unpack .../03-procps_2%3a3.3.17-4_armhf.deb ...
Unpacking procps (2:3.3.17-4) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../04-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../05-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../06-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../07-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../08-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../09-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../10-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../11-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../12-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../13-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../14-cmake-data_3.18.4-2+rpi1_all.deb ...
Unpacking cmake-data (3.18.4-2+rpi1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../15-libicu67_67.1-6_armhf.deb ...
Unpacking libicu67:armhf (67.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../16-libxml2_2.9.10+dfsg-6.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-6.3) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../17-libarchive13_3.4.3-2_armhf.deb ...
Unpacking libarchive13:armhf (3.4.3-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../18-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../19-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../20-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../21-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../22-libssh2-1_1.9.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.9.0-2) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../23-libcurl4_7.74.0-1.1_armhf.deb ...
Unpacking libcurl4:armhf (7.74.0-1.1) ...
Selecting previously unselected package libjsoncpp24:armhf.
Preparing to unpack .../24-libjsoncpp24_1.9.4-4_armhf.deb ...
Unpacking libjsoncpp24:armhf (1.9.4-4) ...
Selecting previously unselected package librhash0:armhf.
Preparing to unpack .../25-librhash0_1.4.1-1_armhf.deb ...
Unpacking librhash0:armhf (1.4.1-1) ...
Selecting previously unselected package libuv1:armhf.
Preparing to unpack .../26-libuv1_1.40.0-1_armhf.deb ...
Unpacking libuv1:armhf (1.40.0-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../27-cmake_3.18.4-2+rpi1_armhf.deb ...
Unpacking cmake (3.18.4-2+rpi1) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../28-d-shlibs_0.98_all.deb ...
Unpacking d-shlibs (0.98) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../29-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../30-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../31-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../32-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../33-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../34-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../35-dh-strip-nondeterminism_1.11.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.11.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../36-libelf1_0.183-1_armhf.deb ...
Unpacking libelf1:armhf (0.183-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../37-dwz_0.13+20210201-1_armhf.deb ...
Unpacking dwz (0.13+20210201-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../38-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../39-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../40-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../41-debhelper_13.3.4_all.deb ...
Unpacking debhelper (13.3.4) ...
Selecting previously unselected package googletest.
Preparing to unpack .../42-googletest_1.10.0.20201025-1.1_all.deb ...
Unpacking googletest (1.10.0.20201025-1.1) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../43-hdf5-helpers_1.10.6+repack-2_armhf.deb ...
Unpacking hdf5-helpers (1.10.6+repack-2) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../44-libaec0_1.0.4-1_armhf.deb ...
Unpacking libaec0:armhf (1.0.4-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../45-libsz2_1.0.4-1_armhf.deb ...
Unpacking libsz2:armhf (1.0.4-1) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../46-libaec-dev_1.0.4-1_armhf.deb ...
Unpacking libaec-dev:armhf (1.0.4-1) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../47-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../48-libboost-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../49-libcurl3-gnutls_7.74.0-1.1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../50-libcurl4-gnutls-dev_7.74.0-1.1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../51-libdeflate0_1.7-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.7-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../52-libdeflate-dev_1.7-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.7-1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../53-libgfortran5_10.2.1-6+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (10.2.1-6+rpi1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../54-libglib2.0-0_2.66.7-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.66.7-2) ...
Selecting previously unselected package libgtest-dev:armhf.
Preparing to unpack .../55-libgtest-dev_1.10.0.20201025-1.1_armhf.deb ...
Unpacking libgtest-dev:armhf (1.10.0.20201025-1.1) ...
Selecting previously unselected package libhdf5-103-1:armhf.
Preparing to unpack .../56-libhdf5-103-1_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-103-1:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-cpp-103-1:armhf.
Preparing to unpack .../57-libhdf5-cpp-103-1_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-fortran-102:armhf.
Preparing to unpack .../58-libhdf5-fortran-102_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-fortran-102:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-100:armhf.
Preparing to unpack .../59-libhdf5-hl-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-fortran-100:armhf.
Preparing to unpack .../60-libhdf5-hl-fortran-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-cpp-100:armhf.
Preparing to unpack .../61-libhdf5-hl-cpp-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../62-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../63-libjpeg62-turbo_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.0.6-2) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../64-libjpeg62-turbo-dev_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:2.0.6-2) ...
Selecting previously unselected package libjpeg-dev:armhf.
Preparing to unpack .../65-libjpeg-dev_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg-dev:armhf (1:2.0.6-2) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../66-libhdf5-dev_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-dev (1.10.6+repack-2) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../67-libhts3_1.11-4_armhf.deb ...
Unpacking libhts3:armhf (1.11-4) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../68-liblzma-dev_5.2.5-1.0_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-1.0) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../69-libhts-dev_1.11-4_armhf.deb ...
Unpacking libhts-dev:armhf (1.11-4) ...
Selecting previously unselected package libpbcopper1.3.0.
Preparing to unpack .../70-libpbcopper1.3.0_1.3.0+dfsg-3_armhf.deb ...
Unpacking libpbcopper1.3.0 (1.3.0+dfsg-3) ...
Selecting previously unselected package libpbbam1.0.6:armhf.
Preparing to unpack .../71-libpbbam1.0.6_1.0.6+dfsg-2+rpi1_armhf.deb ...
Unpacking libpbbam1.0.6:armhf (1.0.6+dfsg-2+rpi1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../72-libssl-dev_1.1.1j-1_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1j-1) ...
Selecting previously unselected package libpbbam-dev.
Preparing to unpack .../73-libpbbam-dev_1.0.6+dfsg-2+rpi1_armhf.deb ...
Unpacking libpbbam-dev (1.0.6+dfsg-2+rpi1) ...
Selecting previously unselected package libpbcopper-dev.
Preparing to unpack .../74-libpbcopper-dev_1.3.0+dfsg-3_armhf.deb ...
Unpacking libpbcopper-dev (1.3.0+dfsg-3) ...
Selecting previously unselected package ninja-build.
Preparing to unpack .../75-ninja-build_1.10.1-1_armhf.deb ...
Unpacking ninja-build (1.10.1-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../76-python3-pkg-resources_52.0.0-3_all.deb ...
Unpacking python3-pkg-resources (52.0.0-3) ...
Selecting previously unselected package meson.
Preparing to unpack .../77-meson_0.56.2-1_all.deb ...
Unpacking meson (0.56.2-1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../78-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
Selecting previously unselected package sbuild-build-depends-pbseqlib-dummy.
Preparing to unpack .../79-sbuild-build-depends-pbseqlib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-pbseqlib-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up hdf5-helpers (1.10.6+repack-2) ...
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.7-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3.4) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up googletest (1.10.0.20201025-1.1) ...
Setting up libaec0:armhf (1.0.4-1) ...
Setting up ninja-build (1.10.1-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libuv1:armhf (1.40.0-1) ...
Setting up libjpeg62-turbo:armhf (1:2.0.6-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.0.6-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libssl-dev:armhf (1.1.1j-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up d-shlibs (0.98) ...
Setting up libgfortran5:armhf (10.2.1-6+rpi1) ...
Setting up libjsoncpp24:armhf (1.9.4-4) ...
Setting up liblzma-dev:armhf (5.2.5-1.0) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up librhash0:armhf (1.4.1-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-1+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up cmake-data (3.18.4-2+rpi1) ...
Setting up libboost-dev:armhf (1.74.0.3+b1) ...
Setting up libdeflate-dev:armhf (1.7-1) ...
Setting up libelf1:armhf (0.183-1) ...
Setting up libpbcopper1.3.0 (1.3.0+dfsg-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libprocps8:armhf (2:3.3.17-4) ...
Setting up libsz2:armhf (1.0.4-1) ...
Setting up libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-2) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libgtest-dev:armhf (1.10.0.20201025-1.1) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libaec-dev:armhf (1.0.4-1) ...
Setting up libjpeg-dev:armhf (1:2.0.6-2) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.1) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpbcopper-dev (1.3.0+dfsg-3) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up libhdf5-103-1:armhf (1.10.6+repack-2) ...
Setting up dwz (0.13+20210201-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up procps (2:3.3.17-4) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ...
Setting up libcurl4:armhf (7.74.0-1.1) ...
Setting up python3.9 (3.9.2-1+rpi1) ...
Setting up libhdf5-hl-100:armhf (1.10.6+repack-2) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.11-4) ...
Setting up python3 (3.9.2-2) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ...
Setting up libpbbam1.0.6:armhf (1.0.6+dfsg-2+rpi1) ...
Setting up libhdf5-fortran-102:armhf (1.10.6+repack-2) ...
Setting up cmake (3.18.4-2+rpi1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ...
Setting up libpbbam-dev (1.0.6+dfsg-2+rpi1) ...
Setting up python3-pkg-resources (52.0.0-3) ...
Setting up meson (0.56.2-1) ...
Setting up debhelper (13.3.4) ...
Setting up libhdf5-dev (1.10.6+repack-2) ...
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 (2.31-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.19-1+rpi1
Package versions: adduser_3.118 apt_2.2.2 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.49 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 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_10.2.1-6+rpi1 d-shlibs_0.98 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.75 debhelper_13.3.4 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.46.2-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-7 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-1 gnupg-l10n_2.2.27-1 gnupg-utils_2.2.27-1 googletest_1.10.0.20201025-1.1 gpg_2.2.27-1 gpg-agent_2.2.27-1 gpg-wks-client_2.2.27-1 gpg-wks-server_2.2.27-1 gpgconf_2.2.27-1 gpgsm_2.2.27-1 gpgv_2.2.27-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20210202-1 libacl1_2.2.53-10 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg6.0_2.2.2 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-7 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_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.1 libcurl4_7.74.0-1.1 libcurl4-gnutls-dev_7.74.0-1.1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.256 libdebhelper-perl_13.3.4 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.183-1 libexpat1_2.2.10-2 libext2fs2_1.46.2-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-7 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-3 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.66.7-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-7 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libgtest-dev_1.10.0.20201025-1.1 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed6_3.7-2.1 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjpeg-dev_1:2.0.6-2 libjpeg62-turbo_1:2.0.6-2 libjpeg62-turbo-dev_1:2.0.6-2 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 libldap-common_2.4.57+dfsg-2 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-7 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.7-2.1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-6 libpam-modules-bin_1.4.0-6 libpam-runtime_1.4.0-6 libpam0g_1.4.0-6 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_5.32.1-3 libpipeline1_1.5.3-1 libprocps8_2:3.3.17-4 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-2 libpython3.9-minimal_3.9.2-1+rpi1 libpython3.9-stdlib_3.9.2-1+rpi1 libreadline8_8.1-1 librhash0_1.4.1-1 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_2.36.1-7 libsqlite3-0_3.34.1-3 libss2_1.46.2-1 libssh2-1_1.9.0-2 libssl-dev_1.1.1j-1 libssl1.1_1.1.1j-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-1+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-7 libuv1_1.40.0-1 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2 linux-libc-dev_5.10.19-1+rpi1 login_1:4.8.1-1 logsave_1.46.2-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 meson_0.56.2-1 mount_2.36.1-7 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 ninja-build_1.10.1-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-3 perl-base_5.32.1-3 perl-modules-5.32_5.32.1-3 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-4 python3_3.9.2-2 python3-minimal_3.9.2-2 python3-pkg-resources_52.0.0-3 python3.9_3.9.2-1+rpi1 python3.9-minimal_3.9.2-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-6 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-7 xz-utils_5.2.5-1.0 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.9FRUhlLK/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 16 12:52:04 2020 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_5.3.4+dfsg-3.dsc
dpkg-source: info: extracting pbseqlib in /<<BUILDDIR>>/pbseqlib-5.3.4+dfsg
dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbseqlib_5.3.4+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hdf5-1.10.1-support.patch
dpkg-source: info: applying hdf5-1.10.0-support.patch
dpkg-source: info: applying meson.patch
dpkg-source: info: applying static+shared_lib.patch
Check disk 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-44c22f35-3f56-4d08-b807-3fd79c889d70
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.4+dfsg-3
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-5.3.4+dfsg'
dh_auto_clean
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
cd obj-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: 0.56.2
Source dir: /<<BUILDDIR>>/pbseqlib-5.3.4+dfsg
Build dir: /<<BUILDDIR>>/pbseqlib-5.3.4+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: libblasr
Project version: 5.3.4
Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial'
C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Raspbian 10.2.1-6+rpi1) 10.2.1 20210110")
C++ linker for the host machine: c++ ld.bfd 2.35.2
Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial'
Host machine cpu family: arm
Host machine cpu: armv8l
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 1.11-4
Library rt found: YES
WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.49.0': disabler arg in dependency.
Run-time dependency HDF5 for cpp found: YES 1.10.6
Configuring LibBlasrConfig.h using configuration
Program tools/check-formatting found: YES (/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg/tools/check-formatting)
WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.53.0': Fallback without variable name.
Run-time dependency GTest found: YES 1.10.0
Build targets in project: 3
WARNING: Project specifies a minimum meson_version '>= 0.46.0' but uses features which were added in newer versions:
* 0.49.0: {'disabler arg in dependency'}
* 0.53.0: {'Fallback without variable name'}
Option buildtype is: plain [default: release]
Found ninja-1.10.1 at /usr/bin/ninja
dh_auto_build -a
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp
../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp
[3/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp
../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp
../hdf/HDFAtom.cpp: In member function ‘void HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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:52:32: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
52 | } catch (H5::Exception e) {
| ^
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[5/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from ../hdf/HDFAlnGroupGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]’:
../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]’
../hdf/HDFAlnGroupGroup.cpp:16:29: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray<T>::Write(const T*, int) [with T = unsigned int]’
../hdf/HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
[6/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp
../hdf/HDFAttributable.cpp: In member function ‘int HDFAttributable::ContainsAttribute(const string&)’:
../hdf/HDFAttributable.cpp:48:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
48 | } catch (H5::Exception e) {
| ^
[7/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp
In file included from ../hdf/HDFAlnInfoGroup.hpp:10,
from ../hdf/HDFAlnInfoGroup.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp
[9/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp
../hdf/HDFData.cpp: In member function ‘int HDFData::BaseInitializeDataset(H5::Group&, const string&)’:
../hdf/HDFData.cpp:37:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]
37 | dataset = hdfFile.openDataSet(_datasetName.c_str());
| ^
In file included from /usr/include/hdf5/serial/H5Cpp.h:45,
from ../hdf/HDFData.hpp:6,
from ../hdf/HDFData.cpp:1:
/usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’
100 | DataSet(const DataSet& original);
| ^~~~~~~
../hdf/HDFData.cpp: In member function ‘int HDFData::InitializeDataset(H5::Group&, const string&)’:
../hdf/HDFData.cpp:52:59: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]
52 | dataset = hdfFile.openDataSet(_datasetName.c_str());
| ^
In file included from /usr/include/hdf5/serial/H5Cpp.h:45,
from ../hdf/HDFData.hpp:6,
from ../hdf/HDFData.cpp:1:
/usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’
100 | DataSet(const DataSet& original);
| ^~~~~~~
[10/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp
[11/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp
../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’:
../hdf/HDFFile.cpp:23:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=]
23 | } catch (FileIException e) {
| ^
../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy]
34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList);
| ^
In file included from /usr/include/hdf5/serial/H5Cpp.h:48,
from ../hdf/HDFFile.hpp:8,
from ../hdf/HDFFile.cpp:1:
/usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’
101 | H5File(const H5File& original);
| ^~~~~~
/usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’:
/usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy]
25 | class H5_DLLCPP H5File : public Group {
| ^~~~~~
In file included from /usr/include/hdf5/serial/H5Cpp.h:47,
from ../hdf/HDFFile.hpp:8,
from ../hdf/HDFFile.cpp:1:
/usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’
57 | Group(const Group& original);
| ^~~~~
../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’:
../hdf/HDFFile.cpp:34:75: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here
34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList);
| ^
../hdf/HDFFile.cpp:35:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=]
35 | } catch (FileIException fileException) {
| ^~~~~~~~~~~~~
[12/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp
../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’:
../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy]
18 | group = fg.openGroup(groupName.c_str());
| ^
In file included from /usr/include/hdf5/serial/H5Cpp.h:47,
from ../hdf/HDFGroup.hpp:9,
from ../hdf/HDFGroup.cpp:1:
/usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’
57 | Group(const Group& original);
| ^~~~~
[13/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFCmpExperimentGroup.hpp:10,
from ../hdf/HDFCmpExperimentGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray<T>::Write(const T*, int) [with T = unsigned char]’
../hdf/HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long long unsigned int]’:
../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray<T>::Write(const T*, int) [with T = char]’
../hdf/HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
[14/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp
../hdf/HDFBaseCallsWriter.cpp: In member function ‘virtual void HDFBaseCallsWriter::Close()’:
../hdf/HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
364 | } catch (H5::Exception e) {
| ^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFBaseCallsWriter.hpp:12,
from ../hdf/HDFBaseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
../hdf/HDFBaseCallsWriter.cpp:342:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]’:
../hdf/HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../hdf/HDFBaseCallsWriter.hpp:11,
from ../hdf/HDFBaseCallsWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[15/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp
[16/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp
[17/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp
[18/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp
../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector<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)
| ^~~~~~~~~~~~~~~~
[19/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp
In file included from ../hdf/HDFScanDataReader.hpp:8,
from ../hdf/HDFPulseDataFile.hpp:10,
from ../hdf/HDFPulseDataFile.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[20/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp
../hdf/HDFPulseCallsWriter.cpp: In member function ‘virtual void HDFPulseCallsWriter::Close()’:
../hdf/HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=]
513 | } catch (H5::Exception e) {
| ^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFPulseCallsWriter.hpp:12,
from ../hdf/HDFPulseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
../hdf/HDFPulseCallsWriter.cpp:492:47: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]’:
../hdf/HDFPulseCallsWriter.cpp:497:39: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
../hdf/HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../hdf/HDFPulseCallsWriter.hpp:11,
from ../hdf/HDFPulseCallsWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp
In file included from ../hdf/HDFScanDataReader.hpp:8,
from ../hdf/HDFScanDataReader.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp
In file included from ../hdf/HDFScanDataWriter.hpp:10,
from ../hdf/HDFScanDataWriter.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[23/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp
In file included from ../hdf/HDFRegionTableReader.hpp:11,
from ../hdf/HDFRegionTableReader.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[24/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp
In file included from ../hdf/HDFWriterBase.hpp:13,
from ../hdf/HDFWriterBase.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from ../hdf/HDFZMWMetricsWriter.cpp:3:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]’:
../hdf/HDFZMWMetricsWriter.cpp:54:27: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
../hdf/HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../hdf/HDFWriterBase.hpp:13,
from ../hdf/HDFZMWMetricsWriter.hpp:8,
from ../hdf/HDFZMWMetricsWriter.cpp:3:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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);
| ^~~~~~~~~
[26/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp
[27/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp
[28/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp
In file included from /usr/include/c++/10/cassert:44,
from ../pbdata/reads/RegionTypeMap.hpp:7,
from ../pbdata/reads/RegionAnnotation.hpp:17,
from ../pbdata/reads/RegionTable.hpp:17,
from ../pbdata/SMRTSequence.hpp:14,
from ../hdf/HDFBasReader.hpp:21,
from ../hdf/HDFUtils.hpp:7,
from ../hdf/HDFUtils.cpp:1:
../hdf/HDFBasReader.hpp: In instantiation of ‘void T_HDFBasReader<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);
| ^~~~~~~~~
[29/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9,
from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits<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:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[30/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp
[31/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits<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:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[32/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from ../hdf/HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
../hdf/HDFZMWWriter.cpp:149:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
146 | } catch (H5::DataSetIException e) {
| ^
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
../hdf/HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../hdf/HDFWriterBase.hpp:13,
from ../hdf/HDFZMWWriter.hpp:12,
from ../hdf/HDFZMWWriter.cpp:5:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/KBandAlign.hpp:10,
from ../alignment/algorithms/alignment/ExtendAlign.hpp:9,
from ../alignment/algorithms/alignment/ExtendAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits<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:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[34/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp
[35/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp
[36/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/GuidedAlign.hpp:11,
from ../alignment/algorithms/alignment/GuidedAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits<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:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[37/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp
[38/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp
[39/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp
[40/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/KBandAlign.hpp:10,
from ../alignment/algorithms/alignment/KBandAlign.cpp:1:
../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits<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:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[41/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp
[42/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp
[43/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp
FAILED: libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o
c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp
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.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp
[45/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp
[46/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp
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 2021-03-19T05:04:51Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 30264
Build-Time: 77
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 324
Job: pbseqlib_5.3.4+dfsg-3
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 424
Source-Version: 5.3.4+dfsg-3
Space: 30264
Status: attempted
Version: 5.3.4+dfsg-3
--------------------------------------------------------------------------------
Finished at 2021-03-19T05:04:51Z
Build needed 00:07:04, 30264k disk space