pbseqlib →
5.3.1+dfsg-2.1+b1 →
armhf → 2019-12-22 05:09:09
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| pbseqlib 5.3.1+dfsg-2.1+b1 (armhf) Sun, 22 Dec 2019 04:42:32 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 5.3.1+dfsg-2.1+b1
Source Version: 5.3.1+dfsg-2.1
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-d0d7ca94-9339-484d-9364-dd847bb1eb1f' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.2 MB in 28s (881 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 980 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.1+dfsg-2.1 (dsc) [2478 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.1+dfsg-2.1 (tar) [968 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pbseqlib 5.3.1+dfsg-2.1 (diff) [8576 B]
Fetched 980 kB in 0s (6636 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-rlg3O5/pbseqlib-5.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-rlg3O5' 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-Swe37z/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-Swe37z/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Swe37z/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2849 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:
libpam-cap netbase
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 27 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (17.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12199 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libhts-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 12~), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-Swe37z/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-Swe37z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Sources [562 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ Packages [633 B]
Fetched 2528 B in 1s (3407 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-9 debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file g++-9 gcc-9
gcc-9-base gettext gettext-base googletest groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libasan5 libatomic1
libboost-dev libboost1.67-dev libbrotli1 libbsd0 libcc1-0 libcroco3
libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libgcc-9-dev libgcc1 libgfortran5
libglib2.0-0 libgomp1 libgssapi-krb5-2 libgtest-dev libhdf5-103
libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpbbam-dev libpbbam0.23.0 libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libstdc++-9-dev libstdc++6
libsub-override-perl libsz2 libtinfo5 libtool libubsan1 libuchardet0 libxml2
m4 man-db mime-support po-debconf python python-minimal python2
python2-minimal python2.7 python2.7-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-9-locales dh-make gcc-9-doc gettext-doc libasprintf-dev
libgettextpo-dev groff libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
krb5-doc krb5-user libhdf5-doc liblzma-doc libssl-doc libstdc++-9-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.67-dev libbrotli1 libbsd0
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2
libgtest-dev libhdf5-103 libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2
libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libnghttp2-14 libpbbam-dev libpbbam0.23.0 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1 libsub-override-perl
libsz2 libtinfo5 libtool libuchardet0 libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal sbuild-build-depends-pbseqlib-dummy sensible-utils
zlib1g-dev
The following packages will be upgraded:
cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libatomic1 libcc1-0 libgcc-9-dev
libgcc1 libgomp1 libstdc++-9-dev libstdc++6 libubsan1
13 upgraded, 84 newly installed, 0 to remove and 14 not upgraded.
Need to get 72.9 MB of archives.
After this operation, 258 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Swe37z/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 9.2.1-21+rpi1 [38.0 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.2.1-21+rpi1 [195 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.2.1-21+rpi1 [37.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.2.1-21+rpi1 [73.8 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.2.1-21+rpi1 [8160 B]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.2.1-21+rpi1 [348 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.2.1-21+rpi1 [112 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.2.1-21+rpi1 [8207 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.2.1-21+rpi1 [1707 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.2.1-21+rpi1 [640 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.2.1-21+rpi1 [7715 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.2.1-21+rpi1 [7458 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.2.1-21+rpi1 [414 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-3 [28.3 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.17-1 [395 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.17-1 [1107 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.17-2 [41.4 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.17-2 [21.1 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.17-1 [1823 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.17-1 [309 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.17-2 [20.9 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.17-2 [20.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.17-2 [41.7 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.17-2 [22.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.2 [174 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-2 [1137 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.2 [1018 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2 [25.3 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf googletest armhf 1.9.0.20190831-1 [622 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b9 [4468 B]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-5 [257 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.3-3 [76.4 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-21+rpi1 [231 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.9.0.20190831-1 [208 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1259 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [121 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2221 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-12 [275 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-12 [4141 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpbbam0.23.0 armhf 0.23.0+dfsg-1+rpi1 [501 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1d-2 [1570 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libpbbam-dev armhf 0.23.0+dfsg-1+rpi1 [85.6 kB]
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Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libgfortran5:armhf (9.2.1-21+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up libubsan1:armhf (9.2.1-21+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up cpp-9 (9.2.1-21+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libcc1-0:armhf (9.2.1-21+rpi1) ...
Setting up libsz2:armhf (1.0.4-1) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libgtest-dev:armhf (1.9.0.20190831-1) ...
Setting up python2.7 (2.7.17-1) ...
Setting up libtool (2.4.6-11) ...
Setting up libpython2-stdlib:armhf (2.7.17-2) ...
Setting up libaec-dev:armhf (1.0.4-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up m4 (1.4.18-4) ...
Setting up python2 (2.7.17-2) ...
Setting up libgcc-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.17-2) ...
Setting up libhdf5-103:armhf (1.10.4+repack-10) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-3) ...
Setting up python (2.7.17-2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gcc-9 (9.2.1-21+rpi1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up libhdf5-cpp-103:armhf (1.10.4+repack-10) ...
Setting up libcurl3-gnutls:armhf (7.67.0-2) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhdf5-dev (1.10.4+repack-10) ...
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 g++-9 (9.2.1-21+rpi1) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libhts2:armhf (1.9-12) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-12) ...
Setting up libpbbam0.23.0:armhf (0.23.0+dfsg-1+rpi1) ...
Setting up libboost-dev:armhf (1.67.0.2+b9) ...
Setting up libpbbam-dev (0.23.0+dfsg-1+rpi1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.2) ...
Setting up dh-exec (0.23.2) ...
Setting up sbuild-build-depends-pbseqlib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-21+rpi1 gcc-9_9.2.1-21+rpi1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-21+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.2 debianutils_4.9 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-21+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-21+rpi1 gcc-9-base_9.2.1-21+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 googletest_1.9.0.20190831-1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-21+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-21+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-5+rpi1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b9 libboost1.67-dev_1.67.0-13 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-21+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.2 libdeflate0_1.3-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21+rpi1 libgcc1_1:9.2.1-21+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-21+rpi1 libglib2.0-0_2.62.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-21+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libgtest-dev_1.9.0.20190831-1 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-12 libhts2_1.9-12 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpbbam-dev_0.23.0+dfsg-1+rpi1 libpbbam0.23.0_0.23.0+dfsg-1+rpi1 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpsl5_0.20.2-2 libpython-stdlib_2.7.17-2 libpython2-stdlib_2.7.17-2 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libsz2_1.0.4-1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-21+rpi1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python_2.7.17-2 python-minimal_2.7.17-2 python2_2.7.17-2 python2-minimal_2.7.17-2 python2.7_2.7.17-1 python2.7-minimal_2.7.17-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Feb 6 07:10:41 2019 UTC
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.1+dfsg-2.1.dsc
dpkg-source: info: extracting pbseqlib in /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg
dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg-2.1.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
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 5.3.1+dfsg-2.1+b1
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-d0d7ca94-9339-484d-9364-dd847bb1eb1f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.1+dfsg-2.1+b1
dpkg-buildpackage: info: source distribution bullseye-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
rm -f libpbdata.a libpbdata.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//hdf clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
rm -f libpbihdf.a libpbihdf.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//alignment clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
rm -f libblasr.a libblasr.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//unittest clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
rm -f -r *.o libblasr-test-runner
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
make[2]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
./configure.py PREFIX=/usr/
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata/LibBlasrConfig.h'
"""
#define USE_PBBAM
"""
writing to 'defines.mk'
"""
CXXFLAGS := -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3
PREFIX_INC := /usr/include
PREFIX_LIB := /usr/lib
SH_LIB_EXT := .so
GTEST_INC ?= /usr/include
GTEST_SRCDIR ?= /usr/src/gtest
HDF5_INC ?= /usr/include/hdf5/serial
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
LIBBLASR_INC ?= ../alignment
LIBBLASR_LIB ?= ../alignment/
LIBPBDATA_INC ?= ../pbdata
LIBPBDATA_LIB ?= ../pbdata/
LIBPBIHDF_INC ?= ../hdf
LIBPBIHDF_LIB ?= ../hdf/
SHELL ?= bash
# Use PREFIX dir, if available.
INCLUDES += ${PREFIX_INC} ../pbdata
LIBS += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_auto_build -- PREFIX_INC=..
make -j4 "INSTALL=install --strip-program=true" PREFIX_INC=..
make[2]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libpbdata
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata LibBlasrConfig.h
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make[4]: 'LibBlasrConfig.h' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTAReader.cpp -o BlasrFASTAReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTQReader.cpp -o BlasrFASTQReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CommandLineParser.cpp -o CommandLineParser.o
In file included from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
../pbdata/FASTASequence.hpp: In instantiation of 'void std::_Construct(_T1*, _Args&& ...) [with _T1 = FASTASequence; _Args = {FASTASequence}]':
/usr/include/c++/9/bits/stl_uninitialized.h:83:18: required from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]'
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*]'
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]'
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator<FASTASequence>]'
/usr/include/c++/9/bits/vector.tcc:659:48: required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; std::vector<_Tp, _Alloc>::size_type = unsigned int]'
/usr/include/c++/9/bits/stl_vector.h:937:4: required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; std::vector<_Tp, _Alloc>::size_type = unsigned int]'
BlasrFASTAReader.cpp:441:26: required from here
../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared 'constexpr DNASequence::DNASequence(const DNASequence&)' is deprecated [-Wdeprecated-copy]
19 | class FASTASequence : public DNASequence
| ^~~~~~~~~~~~~
In file included from ../pbdata/FASTASequence.hpp:13,
from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
../pbdata/DNASequence.hpp:51:18: note: because 'DNASequence' has user-provided 'DNASequence& DNASequence::operator=(const DNASequence&)'
51 | DNASequence &operator=(const DNASequence &rhs);
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:64,
from /usr/include/pbbam/BamRecord.h:12,
from ../pbdata/DNASequence.hpp:17,
from ../pbdata/FASTASequence.hpp:13,
from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
/usr/include/c++/9/bits/stl_construct.h:75:7: note: synthesized method 'constexpr FASTASequence::FASTASequence(const FASTASequence&)' first required here
75 | { ::new(static_cast<void*>(__p)) _T1(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c DNASequence.cpp -o DNASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c GFFFile.cpp -o GFFFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c NucConversion.cpp -o NucConversion.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c StringUtils.cpp -o StringUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MetricField.cpp -o MetricField.o
In file included from SMRTSequence.cpp:3:
SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
| ^~~
SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW'
329 | BLASR_THROW("Base must be in A, C, G, T");
| ^~~~~~~~~~~
SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause
328 | else
| ^~~~
SMRTSequence.cpp: In member function 'void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector<SMRTSequence>&)':
SMRTSequence.cpp:353:25: warning: implicitly-declared 'SMRTSequence::SMRTSequence(const SMRTSequence&)' is deprecated [-Wdeprecated-copy]
353 | for (auto subread : subreads) {
| ^~~~~~~~
SMRTSequence.cpp:208:15: note: because 'SMRTSequence' has user-provided 'SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)'
208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs)
| ^~~~~~~~~~~~
SMRTSequence.cpp:378:25: warning: implicitly-declared 'SMRTSequence::SMRTSequence(const SMRTSequence&)' is deprecated [-Wdeprecated-copy]
378 | for (auto subread : subreads) {
| ^~~~~~~~
SMRTSequence.cpp:208:15: note: because 'SMRTSequence' has user-provided 'SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)'
208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs)
| ^~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c metagenome/TitleTable.cpp -o TitleTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/AcqParams.cpp -o AcqParams.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/BaseFile.cpp -o BaseFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/HoleXY.cpp -o HoleXY.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseFile.cpp -o PulseFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ReadType.cpp -o ReadType.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotation.cpp -o RegionAnnotation.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotations.cpp -o RegionAnnotations.o
reads/RegionAnnotations.cpp: In constructor 'RegionAnnotations::RegionAnnotations(UInt, const std::vector<RegionAnnotation>&, const std::vector<T_RegionType>&)':
reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
14 | for (auto annotation : annotations) {
| ^~~~~~~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<RegionAnnotation> RegionAnnotations::RegionAnnotationsOfType(RegionType) const':
reads/RegionAnnotations.cpp:37:24: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
37 | for (auto ra : table_)
| ^~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
reads/RegionAnnotations.cpp:65:22: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
65 | return hqs_[0];
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
In file included from reads/RegionAnnotations.cpp:3:
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
| ^~~
reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW'
67 | BLASR_THROW("Zmw has more than one HQRegion");
| ^~~~~~~~~~~
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
66 | else
| ^~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<ReadInterval> RegionAnnotations::AdapterIntervals() const':
reads/RegionAnnotations.cpp:84:34: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
84 | for (auto adapter : Adapters()) {
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<ReadInterval> RegionAnnotations::SubreadIntervals(DNALength, bool, bool) const':
reads/RegionAnnotations.cpp:102:42: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
102 | for (auto adapter : Adapters()) {
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp:121:24: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
121 | for (auto insert : inserts) {
| ^~~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTable.cpp -o RegionTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTypeMap.cpp -o RegionTypeMap.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ScanData.cpp -o ScanData.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/AlnGroup.cpp -o AlnGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/MovieInfo.cpp -o MovieInfo.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefGroup.cpp -o RefGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefInfo.cpp -o RefInfo.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReadGroup.cpp -o ReadGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReferenceSequence.cpp -o ReferenceSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMAlignment.cpp -o SAMAlignment.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMHeader.cpp -o SAMHeader.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/BitUtils.cpp -o BitUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTTitle.cpp -o SMRTTitle.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/TimeUtils.cpp -o TimeUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTAReader.cpp -o BlasrFASTAReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTQReader.cpp -o BlasrFASTQReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o
In file included from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
../pbdata/FASTASequence.hpp: In instantiation of 'void std::_Construct(_T1*, _Args&& ...) [with _T1 = FASTASequence; _Args = {FASTASequence}]':
/usr/include/c++/9/bits/stl_uninitialized.h:83:18: required from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]'
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*]'
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<FASTASequence*>; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]'
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator<FASTASequence>]'
/usr/include/c++/9/bits/vector.tcc:659:48: required from 'void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; std::vector<_Tp, _Alloc>::size_type = unsigned int]'
/usr/include/c++/9/bits/stl_vector.h:937:4: required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator<FASTASequence>; std::vector<_Tp, _Alloc>::size_type = unsigned int]'
BlasrFASTAReader.cpp:441:26: required from here
../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared 'constexpr DNASequence::DNASequence(const DNASequence&)' is deprecated [-Wdeprecated-copy]
19 | class FASTASequence : public DNASequence
| ^~~~~~~~~~~~~
In file included from ../pbdata/FASTASequence.hpp:13,
from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
../pbdata/DNASequence.hpp:51:18: note: because 'DNASequence' has user-provided 'DNASequence& DNASequence::operator=(const DNASequence&)'
51 | DNASequence &operator=(const DNASequence &rhs);
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:64,
from /usr/include/pbbam/BamRecord.h:12,
from ../pbdata/DNASequence.hpp:17,
from ../pbdata/FASTASequence.hpp:13,
from ../pbdata/FASTAReader.hpp:7,
from BlasrFASTAReader.cpp:2:
/usr/include/c++/9/bits/stl_construct.h:75:7: note: synthesized method 'constexpr FASTASequence::FASTASequence(const FASTASequence&)' first required here
75 | { ::new(static_cast<void*>(__p)) _T1(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c DNASequence.cpp -o DNASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o
In file included from SMRTSequence.cpp:3:
SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
| ^~~
SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW'
329 | BLASR_THROW("Base must be in A, C, G, T");
| ^~~~~~~~~~~
SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause
328 | else
| ^~~~
SMRTSequence.cpp: In member function 'void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector<SMRTSequence>&)':
SMRTSequence.cpp:353:25: warning: implicitly-declared 'SMRTSequence::SMRTSequence(const SMRTSequence&)' is deprecated [-Wdeprecated-copy]
353 | for (auto subread : subreads) {
| ^~~~~~~~
SMRTSequence.cpp:208:15: note: because 'SMRTSequence' has user-provided 'SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)'
208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs)
| ^~~~~~~~~~~~
SMRTSequence.cpp:378:25: warning: implicitly-declared 'SMRTSequence::SMRTSequence(const SMRTSequence&)' is deprecated [-Wdeprecated-copy]
378 | for (auto subread : subreads) {
| ^~~~~~~~
SMRTSequence.cpp:208:15: note: because 'SMRTSequence' has user-provided 'SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)'
208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs)
| ^~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o
reads/RegionAnnotations.cpp: In constructor 'RegionAnnotations::RegionAnnotations(UInt, const std::vector<RegionAnnotation>&, const std::vector<T_RegionType>&)':
reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
14 | for (auto annotation : annotations) {
| ^~~~~~~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<RegionAnnotation> RegionAnnotations::RegionAnnotationsOfType(RegionType) const':
reads/RegionAnnotations.cpp:37:24: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
37 | for (auto ra : table_)
| ^~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
reads/RegionAnnotations.cpp:65:22: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
65 | return hqs_[0];
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
In file included from reads/RegionAnnotations.cpp:3:
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
8 | std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
| ^~~
reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW'
67 | BLASR_THROW("Zmw has more than one HQRegion");
| ^~~~~~~~~~~
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
66 | else
| ^~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<ReadInterval> RegionAnnotations::AdapterIntervals() const':
reads/RegionAnnotations.cpp:84:34: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
84 | for (auto adapter : Adapters()) {
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp: In member function 'std::vector<ReadInterval> RegionAnnotations::SubreadIntervals(DNALength, bool, bool) const':
reads/RegionAnnotations.cpp:102:42: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
102 | for (auto adapter : Adapters()) {
| ^
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
reads/RegionAnnotations.cpp:121:24: warning: implicitly-declared 'constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)' is deprecated [-Wdeprecated-copy]
121 | for (auto insert : inserts) {
| ^~~~~~~
In file included from ../pbdata/reads/ReadInterval.hpp:4,
from ../pbdata/reads/RegionAnnotations.hpp:10,
from reads/RegionAnnotations.cpp:4:
../pbdata/reads/RegionAnnotation.hpp:115:26: note: because 'RegionAnnotation' has user-provided 'RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)'
115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
| ^~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ScanData.cpp -o ScanData.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o
ar rc libpbdata.a BlasrFASTAReader.o BlasrFASTQReader.o CCSSequence.o ChangeListID.o CommandLineParser.o DNASequence.o FASTASequence.o FASTQSequence.o GFFFile.o MD5Utils.o NucConversion.o PackedDNASequence.o ReverseCompressIndex.o SMRTSequence.o StringUtils.o CmpAlignment.o AfgBasWriter.o MetricField.o MovieAlnIndexLookupTable.o TitleTable.o BlasrQualityValue.o QualityTransform.o AcqParams.o BaseFile.o HoleXY.o PulseBaseCommon.o PulseFile.o ReadType.o RegionAnnotation.o RegionAnnotations.o RegionTable.o RegionTypeMap.o ScanData.o ZMWGroupEntry.o AlnGroup.o MovieInfo.o RefGroup.o RefInfo.o ReadGroup.o ReferenceSequence.o SAMAlignment.o SAMHeader.o SAMKeywordValuePair.o BitUtils.o SMRTReadUtils.o SMRTTitle.o TimeUtils.o
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -o libpbdata.so -Wl,-soname,libpbdata.so BlasrFASTAReader.shared.o BlasrFASTQReader.shared.o CCSSequence.shared.o ChangeListID.shared.o CommandLineParser.shared.o DNASequence.shared.o FASTASequence.shared.o FASTQSequence.shared.o GFFFile.shared.o MD5Utils.shared.o NucConversion.shared.o PackedDNASequence.shared.o ReverseCompressIndex.shared.o SMRTSequence.shared.o StringUtils.shared.o CmpAlignment.shared.o AfgBasWriter.shared.o MetricField.shared.o MovieAlnIndexLookupTable.shared.o TitleTable.shared.o BlasrQualityValue.shared.o QualityTransform.shared.o AcqParams.shared.o BaseFile.shared.o HoleXY.shared.o PulseBaseCommon.shared.o PulseFile.shared.o ReadType.shared.o RegionAnnotation.shared.o RegionAnnotations.shared.o RegionTable.shared.o RegionTypeMap.shared.o ScanData.shared.o ZMWGroupEntry.shared.o AlnGroup.shared.o MovieInfo.shared.o RefGroup.shared.o RefInfo.shared.o ReadGroup.shared.o ReferenceSequence.shared.o SAMAlignment.shared.o SAMHeader.shared.o SAMKeywordValuePair.shared.o BitUtils.shared.o SMRTReadUtils.shared.o SMRTTitle.shared.o TimeUtils.shared.o -lpbbam -lpbbam
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libpbihdf
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//hdf all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataReader.cpp -o HDFScanDataReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
In file included from ../hdf/HDFScanDataReader.hpp:8,
from 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>]':
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 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 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>]':
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 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 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>]':
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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o
In file included from ../hdf/HDFRegionTableReader.hpp:11,
from 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:45:54: 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>]'
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 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);
| ^~~~~~~~~
In file included from ../hdf/HDFWriterBase.hpp:13,
from 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>]':
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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.o
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char*]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string<char>]':
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 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);
| ^~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFCmpExperimentGroup.hpp:10,
from 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from HDFZMWMetricsWriter.cpp:3:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:54:27: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o
In file included from ../hdf/HDFScanDataReader.hpp:8,
from ../hdf/HDFPulseDataFile.hpp:10,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
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 HDFPulseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:492:47: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFPulseCallsWriter.cpp:497:39: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
In file included from ../hdf/HDFPulseCallsWriter.hpp:11,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFFile.cpp -o HDFFile.o
HDFFile.cpp: In member function 'void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)':
HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
23 | } catch (FileIException e) {
| ^
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 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 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);
| ^~~~~
HDFFile.cpp: In member function 'void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)':
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);
| ^
HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
35 | } catch (FileIException fileException) {
| ^~~~~~~~~~~~~
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
364 | } catch (H5::Exception e) {
| ^
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFBaseCallsWriter.hpp:12,
from HDFBaseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:342:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/HDFBaseCallsWriter.hpp:11,
from 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionsWriter.cpp -o HDFRegionsWriter.o
In file included from ../hdf/HDFAlnInfoGroup.hpp:10,
from 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>]':
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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
HDFRegionsWriter.cpp: In member function 'bool HDFRegionsWriter::Write(const std::vector<RegionAnnotation>&)':
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 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)
| ^~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.o
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>]':
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
In file included from /usr/include/hdf5/serial/H5Cpp.h:34,
from ../hdf/HDFAtom.hpp:9,
from 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseWriter.cpp -o HDFPulseWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
In file included from ../hdf/HDFScanDataWriter.hpp:10,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
HDFGroup.cpp: In member function 'int HDFGroup::Initialize(H5::Group&, std::string)':
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 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);
| ^~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFData.cpp -o HDFData.o
In file included from ../hdf/HDFBasReader.hpp:14,
from ../hdf/HDFUtils.hpp:7,
from 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:581:27: required from 'int T_HDFBasReader<T_Sequence>::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string<char>]'
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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o
HDFData.cpp: In member function 'int HDFData::BaseInitializeDataset(H5::Group&, const string&)':
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 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);
| ^~~~~~~
HDFData.cpp: In member function 'int HDFData::InitializeDataset(H5::Group&, const string&)':
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 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);
| ^~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
HDFAlnGroupGroup.cpp:16:29: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]':
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); \
| ^
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 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);
| ^~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
48 | } catch (H5::Exception e) {
| ^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:149:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o
In file included from ../hdf/HDFWriterBase.hpp:13,
from ../hdf/HDFZMWWriter.hpp:12,
from 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.o
In file included from ../hdf/HDFScanDataReader.hpp:8,
from 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>]':
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 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 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>]':
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 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 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>]':
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 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/HDFWriterBase.hpp:13,
from 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>]':
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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o
In file included from ../hdf/HDFRegionTableReader.hpp:11,
from 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:45:54: 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>]'
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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char*]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDFArray.cpp: In member function 'void BufferedHDFArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string<char>]':
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 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);
| ^~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFCmpExperimentGroup.hpp:10,
from 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from HDFZMWMetricsWriter.cpp:3:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:54:27: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o
In file included from ../hdf/HDFWriterBase.hpp:13,
from ../hdf/HDFZMWMetricsWriter.hpp:8,
from 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:40:53: 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 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);
| ^~~~~~~~~
In file included from ../hdf/HDFScanDataReader.hpp:8,
from ../hdf/HDFPulseDataFile.hpp:10,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
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 HDFPulseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:492:47: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFPulseCallsWriter.cpp:497:39: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
In file included from ../hdf/HDFPulseCallsWriter.hpp:11,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFFile.cpp -o HDFFile.shared.o
HDFFile.cpp: In member function 'void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)':
HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
23 | } catch (FileIException e) {
| ^
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 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 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);
| ^~~~~
HDFFile.cpp: In member function 'void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)':
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);
| ^
HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
35 | } catch (FileIException fileException) {
| ^~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
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 HDFBaseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:342:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/HDFBaseCallsWriter.hpp:11,
from 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:40:53: 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 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);
| ^~~~~~~~~
In file included from ../hdf/HDFAlnInfoGroup.hpp:10,
from 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>]':
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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.o
In file included from ../hdf/HDFAlnInfoGroup.hpp:10,
from 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
HDFRegionsWriter.cpp: In member function 'bool HDFRegionsWriter::Write(const std::vector<RegionAnnotation>&)':
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 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)
| ^~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
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>]':
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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);
| ^~~~~~~~~
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>]':
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); \
| ^
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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 HDFAtom.cpp:1:
../hdf/HDFAtom.hpp:52:11: 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>]':
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 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 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>]':
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 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 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>]':
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 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 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>]':
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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o
In file included from ../hdf/HDFScanDataWriter.hpp:10,
from 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
HDFGroup.cpp: In member function 'int HDFGroup::Initialize(H5::Group&, std::string)':
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 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);
| ^~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFData.cpp -o HDFData.shared.o
HDFData.cpp: In member function 'int HDFData::BaseInitializeDataset(H5::Group&, const string&)':
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 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);
| ^~~~~~~
HDFData.cpp: In member function 'int HDFData::InitializeDataset(H5::Group&, const string&)':
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 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);
| ^~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o
In file included from ../hdf/HDFBasReader.hpp:14,
from ../hdf/HDFUtils.hpp:7,
from 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:581:27: required from 'int T_HDFBasReader<T_Sequence>::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string<char>]'
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 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 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:40:53: 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 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 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:40:53: 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 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short int]':
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); \
| ^
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 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);
| ^~~~~~~
BufferedHDF2DArray.cpp: In member function 'void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]':
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); \
| ^
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 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);
| ^~~~~~~
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
HDFAlnGroupGroup.cpp:16:29: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
48 | } catch (H5::Exception e) {
| ^
ar rc libpbihdf.a HDFScanDataReader.o HDFWriterBase.o DatasetCollection.o HDFRegionTableReader.o HDFNewBasReader.o BufferedHDFArray.o HDFBaxWriter.o HDFCmpExperimentGroup.o HDFZMWMetricsWriter.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFCmpSupportedFields.o HDFBaseCallsWriter.o HDFZMWReader.o HDFFile.o HDFAlnInfoGroup.o HDFRegionsWriter.o HDFAtom.o HDFScanDataWriter.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFAlnGroupGroup.o HDFData.o HDFZMWWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o HDFAttributable.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:149:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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]':
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: 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 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:40:53: 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 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);
| ^~~~~~~~~
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFScanDataReader.shared.o HDFWriterBase.shared.o DatasetCollection.shared.o HDFRegionTableReader.shared.o HDFNewBasReader.shared.o BufferedHDFArray.shared.o HDFBaxWriter.shared.o HDFCmpExperimentGroup.shared.o HDFZMWMetricsWriter.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFBaseCallsWriter.shared.o HDFZMWReader.shared.o HDFFile.shared.o HDFAlnInfoGroup.shared.o HDFRegionsWriter.shared.o HDFAtom.shared.o HDFScanDataWriter.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o HDFZMWWriter.shared.o HDFPulseH5Writer.shared.o BufferedHDF2DArray.shared.o HDFAttributable.shared.o -lpbbam -lpbbam -lpbdata -lhdf5 -lhdf5_cpp
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libblasr
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//alignment all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c MappingMetrics.cpp -o MappingMetrics.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from 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++/9/bits/alloc_traits.h:484:4: 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++/9/bits/stl_vector.h:1189:30: 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 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 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++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4,
from algorithms/alignment/AlignmentUtils.cpp:1:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method 'blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)' first required here
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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++/9/bits/alloc_traits.h:484:4: required from 'static void std::allocator_traits<std::allocator<_Tp> >::construct(std::allocator_traits<std::allocator<_Tp> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_Tp> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]'
/usr/include/c++/9/bits/stl_vector.h:1189:30: 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 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 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++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/vector:64,
from ../alignment/algorithms/alignment/ExtendAlign.hpp:6,
from algorithms/alignment/ExtendAlign.cpp:1:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method 'blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)' first required here
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/GuidedAlign.hpp:11,
from 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++/9/bits/alloc_traits.h:484:4: 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++/9/bits/stl_vector.h:1189:30: 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 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 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++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from /usr/include/c++/9/bits/locale_classes.h:40,
from /usr/include/c++/9/bits/ios_base.h:41,
from /usr/include/c++/9/ios:42,
from /usr/include/c++/9/ostream:38,
from ../alignment/algorithms/alignment/GuidedAlign.hpp:6,
from algorithms/alignment/GuidedAlign.cpp:1:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method 'blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)' first required here
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/KBandAlign.hpp:10,
from 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++/9/bits/alloc_traits.h:484:4: required from 'static void std::allocator_traits<std::allocator<_Tp> >::construct(std::allocator_traits<std::allocator<_Tp> >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits<std::allocator<_Tp> >::allocator_type = std::allocator<blasr::CompSeqAlignment>]'
/usr/include/c++/9/bits/stl_vector.h:1189:30: 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 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 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++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/vector:64,
from ../alignment/algorithms/alignment/KBandAlign.hpp:7,
from algorithms/alignment/KBandAlign.cpp:1:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method 'blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)' first required here
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/Coordinate.cpp -o Coordinate.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9,
from 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++/9/bits/alloc_traits.h:484:4: 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++/9/bits/stl_vector.h:1189:30: 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 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 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++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4,
from algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method 'blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)' first required here
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
In file included from ../alignment/bwt/BWT.hpp:9,
from ../alignment/algorithms/anchoring/BWTSearch.hpp:6,
from 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);
| ^
make[4]: *** [/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment//../rules.mk:20: BWTSearch.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
make[3]: *** [makefile:23: libblasr] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make[2]: *** [makefile:10: all] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_auto_build: make -j4 "INSTALL=install --strip-program=true" PREFIX_INC=.. returned exit code 2
make[1]: *** [debian/rules:31: override_dh_auto_build] Error 255
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make: *** [debian/rules:25: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-12-22T05:09:04Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 751
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 790
Job: pbseqlib_5.3.1+dfsg-2.1
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1592
Source-Version: 5.3.1+dfsg-2.1
Space: 0
Status: failed
Version: 5.3.1+dfsg-2.1+b1
--------------------------------------------------------------------------------
Finished at 2019-12-22T05:09:04Z
Build needed 00:00:00, 0k disc space