https://launchpad.net/ubuntu/+source/pbseqlib/5.3.5+dfsg-2build1/+build/22612920 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-026 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 Buildd toolchain package versions: launchpad-buildd_205~511~ubuntu18.04.1 python3-lpbuildd_205~511~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 10 Dec 17:13:55 ntpdate[1742]: adjust time server 10.131.248.1 offset -0.003018 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22612920 --image-type chroot /home/buildd/filecache-default/b0c128df17a460089eca69348f06144377489985 Creating target for build PACKAGEBUILD-22612920 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22612920 Starting target for build PACKAGEBUILD-22612920 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22612920 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22612920 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22612920 Updating target for build PACKAGEBUILD-22612920 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 Packages [1399 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe amd64 Packages [13.7 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5552 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 Packages [112 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [46.7 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 Packages [632 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 22.9 MB in 2s (9831 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libssl1.1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 108 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 84.3 MB of archives. After this operation, 354 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main amd64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam0g amd64 1.4.0-10ubuntu2 [61.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt-dev amd64 1:4.4.26-1 [112 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt1 amd64 1:4.4.26-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 base-files amd64 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 debianutils amd64 5.5-1ubuntu1 [107 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 bash amd64 5.1-5ubuntu1 [771 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdutils amd64 1:2.37.2-4ubuntu1 [80.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libgpg-error0 amd64 1.42-3 [68.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcrypt20 amd64 1.9.4-3ubuntu2 [515 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 bzip2 amd64 1.0.8-5 [34.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libbz2-1.0 amd64 1.0.8-5 [34.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libcc1-0 amd64 11.2.0-12ubuntu1 [53.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11-base amd64 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-s1 amd64 11.2.0-12ubuntu1 [45.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libgomp1 amd64 11.2.0-12ubuntu1 [117 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libitm1 amd64 11.2.0-12ubuntu1 [30.0 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libatomic1 amd64 11.2.0-12ubuntu1 [9998 B] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 libasan6 amd64 11.2.0-12ubuntu1 [2282 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 liblsan0 amd64 11.2.0-12ubuntu1 [976 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 libtsan0 amd64 11.2.0-12ubuntu1 [2259 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libubsan1 amd64 11.2.0-12ubuntu1 [922 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libquadmath0 amd64 11.2.0-12ubuntu1 [154 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 g++-11 amd64 11.2.0-12ubuntu1 [11.4 MB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++-11-dev amd64 11.2.0-12ubuntu1 [2098 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-11-dev amd64 11.2.0-12ubuntu1 [2532 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11 amd64 11.2.0-12ubuntu1 [20.1 MB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 cpp-11 amd64 11.2.0-12ubuntu1 [9962 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++6 amd64 11.2.0-12ubuntu1 [656 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 libisl23 amd64 0.24-2 [728 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpc3 amd64 1.2.1-1 [46.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [324 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf0 amd64 2.37-10ubuntu1 [103 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf-nobfd0 amd64 2.37-10ubuntu1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 libbinutils amd64 2.37-10ubuntu1 [653 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-common amd64 2.37-10ubuntu1 [213 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils amd64 2.37-10ubuntu1 [3192 B] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-x86-64-linux-gnu amd64 2.37-10ubuntu1 [2314 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libssl3 amd64 3.0.0-1ubuntu2 [1896 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libblkid1 amd64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libuuid1 amd64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main amd64 libcryptsetup12 amd64 2:2.4.2-1ubuntu4 [208 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libidn2-0 amd64 2.3.2-2 [66.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libp11-kit0 amd64 0.24.0-6 [252 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main amd64 libtasn1-6 amd64 4.18.0-4 [42.9 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libgnutls30 amd64 3.7.2-2ubuntu1 [957 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-sysv amd64 249.5-2ubuntu2 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-timesyncd amd64 249.5-2ubuntu2 [30.9 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libapparmor1 amd64 3.0.3-0ubuntu5 [38.0 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libip4tc2 amd64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 libkmod2 amd64 28-1ubuntu5 [48.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libpcre2-8-0 amd64 10.39-3 [220 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libselinux1 amd64 3.3-1build1 [74.5 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libmount1 amd64 2.37.2-4ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libseccomp2 amd64 2.5.2-2ubuntu2 [48.3 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 login amd64 1:4.8.1-2ubuntu1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 util-linux amd64 2.37.2-4ubuntu1 [1063 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 mount amd64 2.37.2-4ubuntu1 [114 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd amd64 249.5-2ubuntu2 [4542 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsystemd0 amd64 249.5-2ubuntu2 [317 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libudev1 amd64 249.5-2ubuntu2 [77.6 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main amd64 libapt-pkg6.0 amd64 2.3.13 [904 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 dpkg amd64 1.20.9ubuntu3 [1266 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-3 [91.8 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 grep amd64 3.7-1 [156 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 libncurses6 amd64 6.3-1 [111 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 libncursesw6 amd64 6.3-1 [147 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libtinfo6 amd64 6.3-1 [104 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-bin amd64 6.3-1 [184 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 sed amd64 4.8-1 [188 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 init-system-helpers all 1.61 [39.3 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-base all 6.3-1 [19.9 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgv amd64 2.2.27-2ubuntu1 [137 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main amd64 apt amd64 2.3.13 [1387 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main amd64 libsepol2 amd64 3.3-1 [281 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:77 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage2 amd64 3.3-1build1 [92.4 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main amd64 passwd amd64 1:4.8.1-2ubuntu1 [765 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules-bin amd64 1.4.0-10ubuntu2 [37.6 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules amd64 1.4.0-10ubuntu2 [280 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main amd64 logsave amd64 1.46.4-1ubuntu1 [10.9 kB] Get:82 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amd64 libdpkg-perl all 1.20.9ubuntu3 [235 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main amd64 make amd64 4.3-4ubuntu2 [179 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main amd64 lto-disabled-list all 17 [12.1 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg amd64 2.2.27-2ubuntu1 [518 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgconf amd64 2.2.27-2ubuntu1 [93.9 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg-agent amd64 2.2.27-2ubuntu1 [209 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.22-1 [6450 B] Get:109 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 linux-libc-dev amd64 5.15.0-13.13 [1273 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main amd64 lockfile-progs amd64 0.1.19 [10.0 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main amd64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 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Setting up libasan6:amd64 (11.2.0-12ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 10 17:14:16 UTC 2021. Universal Time is now: Fri Dec 10 17:14:16 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:amd64 (6.3-1) ... Setting up libquadmath0:amd64 (11.2.0-12ubuntu1) ... Setting up libmpc3:amd64 (1.2.1-1) ... Setting up systemd-timesyncd (249.5-2ubuntu2) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:amd64 (11.2.0-12ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:amd64 (1.46.4-1ubuntu1) ... Setting up libncursesw6:amd64 (6.3-1) ... Setting up libdpkg-perl (1.20.9ubuntu3) ... Setting up logsave (1.46.4-1ubuntu1) ... Setting up libubsan1:amd64 (11.2.0-12ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:amd64 (1:4.4.26-1) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libbinutils:amd64 (2.37-10ubuntu1) ... Setting up libisl23:amd64 (0.24-2) ... Setting up openssl (3.0.0-1ubuntu2) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libcc1-0:amd64 (11.2.0-12ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up liblsan0:amd64 (11.2.0-12ubuntu1) ... Setting up libitm1:amd64 (11.2.0-12ubuntu1) ... Setting up libgdbm6:amd64 (1.22-1) ... Setting up libtsan0:amd64 (11.2.0-12ubuntu1) ... Setting up libctf0:amd64 (2.37-10ubuntu1) ... Setting up cpp-11 (11.2.0-12ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up e2fsprogs (1.46.4-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:amd64 (1.22-1) ... Setting up libgcc-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.37-10ubuntu1) ... Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... Setting up libstdc++-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up gcc-11 (11.2.0-12ubuntu1) ... Setting up g++-11 (11.2.0-12ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22612920 amd64 jammy-proposed -c chroot:build-PACKAGEBUILD-22612920 --arch=amd64 --dist=jammy-proposed --nolog -A pbseqlib_5.3.5+dfsg-2build1.dsc Initiating build PACKAGEBUILD-22612920 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lcy02-amd64-026.buildd +==============================================================================+ | pbseqlib 5.3.5+dfsg-2build1 (amd64) Fri, 10 Dec 2021 17:14:19 +0000 | +==============================================================================+ Package: pbseqlib Version: 5.3.5+dfsg-2build1 Source Version: 5.3.5+dfsg-2build1 Distribution: jammy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22612920/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbseqlib_5.3.5+dfsg-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pbseqlib-uL03l3/pbseqlib-5.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbseqlib-uL03l3' with '<>' +------------------------------------------------------------------------------+ | 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 '/<>/resolver-CF0FHb/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. Ign:1 copy:/<>/resolver-CF0FHb/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CF0FHb/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-CF0FHb/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CF0FHb/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-CF0FHb/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... 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: libssl1.1 systemd-timesyncd 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 0 not upgraded. Need to get 650 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-CF0FHb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [650 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 650 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13453 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libpbcopper-dev, libhts-dev Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, meson, pkg-config, cmake, googletest, libgtest-dev, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libpbcopper-dev, libhts-dev dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<>/resolver-CF0FHb/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. Ign:1 copy:/<>/resolver-CF0FHb/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CF0FHb/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-CF0FHb/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CF0FHb/apt_archive ./ Sources [570 B] Get:5 copy:/<>/resolver-CF0FHb/apt_archive ./ Packages [648 B] Fetched 2181 B in 0s (0 B/s) Reading package lists... 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: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.74-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgtest-dev libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp24 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpbbam-dev libpbbam1.6.0 libpbcopper-dev libpbcopper1.8.0 libpbcopper1.9.3 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson ninja-build pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libhdf5-doc liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools python3.9-venv python3.9-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.74-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgtest-dev libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp24 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpbbam-dev libpbbam1.6.0 libpbcopper-dev libpbcopper1.8.0 libpbcopper1.9.3 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson ninja-build pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal sbuild-build-depends-pbseqlib-dummy zlib1g-dev 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 62.7 MB of archives. After this operation, 340 MB of additional disk space will be used. Get:1 copy:/<>/resolver-CF0FHb/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [738 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 libpython3.9-minimal amd64 3.9.9-1build1 [790 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libexpat1 amd64 2.4.1-3 [90.1 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 python3.9-minimal amd64 3.9.9-1build1 [2072 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-minimal amd64 3.9.7-4 [24.7 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 media-types all 4.0.0 [22.2 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpdec3 amd64 2.5.1-2build1 [86.8 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 libpython3.9-stdlib amd64 3.9.9-1build1 [1807 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 python3.9 amd64 3.9.9-1build1 [437 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpython3-stdlib amd64 3.9.7-4 [7298 B] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3 amd64 3.9.7-4 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdextrautils amd64 2.37.2-4ubuntu1 [71.1 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libuchardet0 amd64 0.0.7-1build1 [76.7 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 groff-base amd64 1.22.4-7 [956 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 libpipeline1 amd64 1.5.4-1 [23.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 man-db amd64 2.9.4-2build1 [1180 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libelf1 amd64 0.186-1 [51.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libglib2.0-0 amd64 2.70.2-1 [1436 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 libicu67 amd64 67.1-7ubuntu1 [10.1 MB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 libxml2 amd64 2.9.12+dfsg-5 [761 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-pkg-resources all 59.4.0-1 [132 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic-mgc amd64 1:5.41-2 [257 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic1 amd64 1:5.41-2 [87.3 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 file amd64 1:5.41-2 [21.5 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext-base amd64 0.21-4ubuntu3 [36.6 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 libpsl5 amd64 0.21.0-1.2build1 [57.5 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 libuv1 amd64 1.42.0-1 [92.3 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 libsigsegv2 amd64 2.13-1ubuntu2 [14.6 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 m4 amd64 1.4.18-5ubuntu1 [199 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 autoconf all 2.71-2 [338 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 automake all 1:1.16.5-1.1 [558 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 autopoint all 0.21-4ubuntu3 [422 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive13 amd64 3.4.3-2build1 [362 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 libbrotli1 amd64 1.0.9-2build4 [315 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-2build1 [20.6 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 libsasl2-2 amd64 2.1.27+dfsg2-2build1 [53.9 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 libldap-2.5-0 amd64 2.5.6+dfsg-1~exp1ubuntu1 [186 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libnghttp2-14 amd64 1.43.0-1build2 [76.2 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build3 [58.3 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libssh-4 amd64 0.9.6-1build1 [184 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcurl4 amd64 7.74.0-1.3ubuntu3 [274 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libjsoncpp24 amd64 1.9.4-5 [80.3 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 librhash0 amd64 1.4.2-1 [125 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/universe amd64 dh-elpa-helper all 2.0.9ubuntu1 [7610 B] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 emacsen-common all 3.0.4 [14.9 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 cmake-data all 3.21.4-1ubuntu1 [1886 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 cmake amd64 3.21.4-1ubuntu1 [5004 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/universe amd64 d-shlibs all 0.104 [10.2 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 libtool all 2.4.6-15build1 [164 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 libdw1 amd64 0.186-1 [251 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 debugedit amd64 1:5.0-3 [47.0 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main amd64 dwz amd64 0.14-1build1 [104 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext amd64 0.21-4ubuntu3 [824 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 debhelper all 13.5.2ubuntu1 [926 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/universe amd64 googletest all 1.11.0-3 [541 kB] Get:65 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 hdf5-helpers amd64 1.10.7+repack-4ubuntu2 [14.2 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/universe amd64 libaec0 amd64 1.0.6-1 [20.1 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 libboost1.74-dev amd64 1.74.0-13ubuntu1 [9618 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libboost-dev amd64 1.74.0.3ubuntu6 [3452 B] Get:69 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcurl3-gnutls amd64 7.74.0-1.3ubuntu3 [267 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3ubuntu3 [361 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 libdeflate0 amd64 1.8-1ubuntu1 [56.4 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 libdeflate-dev amd64 1.8-1ubuntu1 [48.2 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 libgfortran5 amd64 11.2.0-12ubuntu1 [794 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/universe amd64 libgtest-dev amd64 1.11.0-3 [250 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/universe amd64 libsz2 amd64 1.0.6-1 [5354 B] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libhdf5-103-1 amd64 1.10.7+repack-4ubuntu2 [1295 kB] Get:77 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libhdf5-cpp-103-1 amd64 1.10.7+repack-4ubuntu2 [129 kB] Get:78 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libhdf5-fortran-102 amd64 1.10.7+repack-4ubuntu2 [90.9 kB] Get:79 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libhdf5-hl-100 amd64 1.10.7+repack-4ubuntu2 [59.1 kB] Get:80 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 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libpbcopper-dev amd64 1.9.3+dfsg-2 [969 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/universe amd64 ninja-build amd64 1.10.1-1 [111 kB] Get:101 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-lib2to3 all 3.9.9-3 [77.7 kB] Get:102 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-distutils all 3.9.9-3 [144 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/universe amd64 meson all 0.60.2-1 [514 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main amd64 pkg-config amd64 0.29.2-1ubuntu2 [48.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.7 MB in 0s (143 MB/s) Selecting previously unselected package libpython3.9-minimal:amd64. 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Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up python3.9 (3.9.9-1build1) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3ubuntu3) ... Setting up python3 (3.9.7-4) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3ubuntu3) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up cmake (3.21.4-1ubuntu1) ... Setting up python3-lib2to3 (3.9.9-3) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4ubuntu2) ... 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Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic amd64 (x86_64) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.20.9ubuntu3 g++-11_11.2.0-12ubuntu1 gcc-11_11.2.0-12ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 linux-libc-dev_5.15.0-13.13 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-5ubuntu1 binutils_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 binutils-x86-64-linux-gnu_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 cmake_3.21.4-1ubuntu1 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perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkg-config_0.29.2-1ubuntu2 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 python3_3.9.7-4 python3-distutils_3.9.9-3 python3-lib2to3_3.9.9-3 python3-minimal_3.9.7-4 python3-pkg-resources_59.4.0-1 python3.9_3.9.9-1build1 python3.9-minimal_3.9.9-1build1 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 systemd_249.5-2ubuntu2 systemd-sysv_249.5-2ubuntu2 systemd-timesyncd_249.5-2ubuntu2 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Dec 10 17:12:48 2021 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.5+dfsg-2build1.dsc dpkg-source: info: extracting pbseqlib in /<>/pbseqlib-5.3.5+dfsg dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking pbseqlib_5.3.5+dfsg-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hdf5-1.10.1-support.patch dpkg-source: info: applying hdf5-1.10.0-support.patch dpkg-source: info: applying meson.patch dpkg-source: info: applying static+shared_lib.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22612920 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22612920 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22612920 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.5+dfsg-2build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/pbseqlib-5.3.5+dfsg' dh_auto_clean find -name defines.mk -delete rm -f pbdata/libconfig.h make[1]: Leaving directory '/<>/pbseqlib-5.3.5+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 0.60.2 Source dir: /<>/pbseqlib-5.3.5+dfsg Build dir: /<>/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: libblasr Project version: 5.3.5 C++ compiler for the host machine: c++ (gcc 11.2.0 "c++ (Ubuntu 11.2.0-12ubuntu1) 11.2.0") C++ linker for the host machine: c++ ld.bfd 2.37 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Run-time dependency pbbam found: YES 1.6.0 Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.13+ds Library rt found: YES Run-time dependency HDF5 for cpp found: YES 1.10.7 Configuring LibBlasrConfig.h using configuration Program tools/check-formatting found: YES (/<>/pbseqlib-5.3.5+dfsg/tools/check-formatting) Run-time dependency GTest found: YES 1.11.0 Build targets in project: 3 libblasr 5.3.5 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:82:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 82 | DEFINE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:83:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 83 | DEFINE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:84:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 84 | DEFINE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:85:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 85 | DEFINE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:86:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 86 | DEFINE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:87:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 87 | DEFINE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDF2DArray.cpp:88:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ROW’ 88 | DEFINE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/BufferedHDF2DArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:67:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 67 | DEFINE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:68:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 68 | DEFINE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = char*]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:69:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 69 | DEFINE_TYPED_CREATE_ARRAY(char *, H5::StrType(0, H5T_VARIABLE)) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned char]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:70:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 70 | DEFINE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:71:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 71 | DEFINE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = float]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:72:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 72 | DEFINE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = short unsigned int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ | ^ ../hdf/BufferedHDFArray.cpp:73:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ARRAY’ 73 | DEFINE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = std::__cxx11::basic_string]’: ../hdf/BufferedHDFArray.cpp:79:86: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), varStrType, space, cparms); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/BufferedHDFArray.hpp:10, from ../hdf/BufferedHDFArray.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp [5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp [6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:9:92: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 9 | attribute = object.createAttribute(atomName.c_str(), strType, H5::DataSpace(H5S_SCALAR)); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:20:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 20 | DEFINE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:21:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 21 | DEFINE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:22:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 22 | DEFINE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:23:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 23 | DEFINE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:24:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 24 | DEFINE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:25:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 25 | DEFINE_TYPED_CREATE_ATOM(uint16_t, H5::PredType::NATIVE_UINT16) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::TypedCreate(H5::H5Object&, const string&, H5::DataSpace&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:17:90: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 17 | attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \ | ^ ../hdf/HDFAtom.cpp:26:1: note: in expansion of macro ‘DEFINE_TYPED_CREATE_ATOM’ 26 | DEFINE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:174:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:175:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:176:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = unsigned char; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:177:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = long unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:178:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:179:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:180:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:181:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:182:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:51:23: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 51 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5File&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:65:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 65 | attribute = group.group.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:84:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 84 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, std::vector&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:93:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 93 | attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 | H5::DataSpace(1, &length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAtom.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:183:16: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFAtom.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [7/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAlnInfoGroup.cpp:44:23: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFAlnInfoGroup.hpp:8, from ../hdf/HDFAlnInfoGroup.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [8/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp [9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp ../hdf/HDFData.cpp: In member function ‘int HDFData::BaseInitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:37:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 37 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ ../hdf/HDFData.cpp: In member function ‘int HDFData::InitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:52:59: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 52 | dataset = hdfFile.openDataSet(_datasetName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from ../hdf/HDFData.hpp:6, from ../hdf/HDFData.cpp:1: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ [10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp [11/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFFile.hpp:8, from ../hdf/HDFFile.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:34:75: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ [12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp ../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’: ../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 18 | group = fg.openGroup(groupName.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from ../hdf/HDFGroup.hpp:9, from ../hdf/HDFGroup.cpp:1: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ [13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp In file included from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp [15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp [16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp [17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFPulseDataFile.hpp:7, from ../hdf/HDFPulseDataFile.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp [19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp ../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: ../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 44 | for (auto annotation : annotations) | ^~~~~~~~~~~ In file included from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFWriterBase.hpp:17, from ../hdf/HDFRegionsWriter.hpp:13, from ../hdf/HDFRegionsWriter.cpp:3: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:26:33: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:29:33: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFScanDataReader.cpp:33:39: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFScanDataReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFPulseCallsWriter.hpp:11, from ../hdf/HDFPulseCallsWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../hdf/HDFRegionTableReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFRegionTableReader.cpp:31:31: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../hdf/HDFRegionTableReader.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFWriterBase.cpp:49:29: required from here ../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp [26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp [27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWMetricsWriter.hpp:8, from ../hdf/HDFZMWMetricsWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWMetricsWriter.hpp:6, from ../hdf/HDFZMWMetricsWriter.cpp:3: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/string:41, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp [30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/string:41, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/11/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, from ../pbdata/reads/RegionTable.hpp:17, from ../pbdata/SMRTSequence.hpp:14, from ../hdf/HDFBasReader.hpp:21, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFBasReader.hpp: In instantiation of ‘void T_HDFBasReader::GetMinMaxHoleNumber(UInt&, UInt&) [with T_Sequence = FASTASequence; UInt = unsigned int]’: ../hdf/HDFUtils.cpp:41:38: required from here ../hdf/HDFBasReader.hpp:1233:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 1233 | assert(nReads >= 0); | ~~~~~~~^~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = FASTASequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = FASTASequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFUtils.cpp:39:29: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../hdf/HDFUtils.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWWriter.hpp:12, from ../hdf/HDFZMWWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/BufferedHDF2DArray.hpp:8, from ../hdf/HDFZMWWriter.hpp:10, from ../hdf/HDFZMWWriter.cpp:5: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/vector:64, from ../alignment/algorithms/alignment/ExtendAlign.hpp:6, from ../alignment/algorithms/alignment/ExtendAlign.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/string:41, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/ostream:38, from ../alignment/algorithms/alignment/GuidedAlign.hpp:6, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp [36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp [37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp [38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp [39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp [40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/vector:64, from ../alignment/algorithms/alignment/KBandAlign.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 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libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp ../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: ../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); | ^~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/datastructures/alignment/Alignment.cpp:2: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ [54/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp [55/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial 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libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp [59/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp [60/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp [61/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp [62/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp [63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp [64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp [65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp [66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ ../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here ../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ ../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/string:41, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from ../alignment/format/CompareSequencesPrinter.hpp:4, from ../alignment/format/CompareSequencesPrinter.cpp:1: /usr/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [67/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp [68/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o -c ../alignment/format/SAMPrinter.cpp [69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp [70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -c ../alignment/query/SequentialZmwGroupQuery.cpp [71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -c ../alignment/query/PbiFilterZmwGroupQuery.cpp [72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, from ../alignment/format/SAMHeaderPrinter.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [73/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../alignment/files/ReaderAgglomerate.cpp:250:47: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [74/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o -MF libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o -c ../alignment/qvs/QualityValueProfile.cpp [75/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/11/cassert:44, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, from ../alignment/simulator/LengthHistogram.hpp:8, from ../alignment/simulator/LengthHistogram.cpp:1: ../alignment/simulator/CDFMap.hpp: In instantiation of ‘int CDFMap::SelectRandomValue(T_Data&) [with T_Data = int]’: ../alignment/simulator/LengthHistogram.cpp:27:87: required from here ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ [76/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp [77/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -c ../alignment/simulator/ContextSample.cpp [78/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp [79/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp [80/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -c ../alignment/tuples/BaseTuple.cpp [81/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o -c ../alignment/simulator/ContextSet.cpp [82/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -c ../alignment/tuples/TupleMetrics.cpp [83/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o -c ../alignment/simulator/QualitySample.cpp [84/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o -c ../alignment/utils/BlasrFileUtils.cpp [85/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o -c ../alignment/utils/LogUtils.cpp [86/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o -c ../alignment/utils/PhredUtils.cpp [87/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.cpp [88/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o -c ../alignment/utils/RangeUtils.cpp [89/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp [90/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o -c ../alignment/statistics/LookupAnchorDistribution.cpp [91/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp [92/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o -c ../pbdata/loadpulses/MetricField.cpp [93/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp [94/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp [95/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -c ../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp [96/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp [97/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o -c ../pbdata/reads/AcqParams.cpp [98/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp [99/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp [100/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp [101/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp [102/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp [103/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp [104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o -c ../pbdata/reads/RegionAnnotation.cpp [105/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o -c ../pbdata/reads/BaseFile.cpp [106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { | ^~~~~~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::RegionAnnotationsOfType(RegionType) const’: ../pbdata/reads/RegionAnnotations.cpp:37:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 37 | for (auto ra : table_) | ^~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘RegionAnnotation RegionAnnotations::TheHQRegion() const’: ../pbdata/reads/RegionAnnotations.cpp:65:22: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 65 | return hqs_[0]; | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::AdapterIntervals() const’: ../pbdata/reads/RegionAnnotations.cpp:85:34: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 85 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp: In member function ‘std::vector RegionAnnotations::SubreadIntervals(DNALength, bool, bool) const’: ../pbdata/reads/RegionAnnotations.cpp:103:42: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 103 | for (auto adapter : Adapters()) { | ^ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ ../pbdata/reads/RegionAnnotations.cpp:122:24: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 122 | for (auto insert : inserts) { | ^~~~~~~ In file included from ../pbdata/reads/ReadInterval.hpp:4, from ../pbdata/reads/RegionAnnotations.hpp:10, from ../pbdata/reads/RegionAnnotations.cpp:4: ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ [107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp [108/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp [109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp [110/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp [111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp [112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp [113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp [114/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp [115/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp [116/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp [117/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp [118/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp [119/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp [120/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -c ../pbdata/sam/SAMAlignment.cpp [121/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -c ../pbdata/sam/SAMKeywordValuePair.cpp [122/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o -c ../pbdata/utils/SMRTTitle.cpp [123/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o -c ../pbdata/utils/TimeUtils.cpp [124/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp [125/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp [126/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o -c ../pbdata/ChangeListID.cpp [127/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp In file included from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/FASTASequence.hpp: In instantiation of ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = FASTASequence; _Args = {FASTASequence}]’: /usr/include/c++/11/bits/stl_uninitialized.h:92:18: required from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]’ /usr/include/c++/11/bits/stl_uninitialized.h:151:15: required from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*]’ /usr/include/c++/11/bits/stl_uninitialized.h:333:37: required from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]’ /usr/include/c++/11/bits/stl_uninitialized.h:355:2: required from ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator]’ /usr/include/c++/11/bits/vector.tcc:659:48: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ /usr/include/c++/11/bits/stl_vector.h:940:4: required from ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ ../pbdata/BlasrFASTAReader.cpp:441:21: required from here ../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] 19 | class FASTASequence : public DNASequence | ^~~~~~~~~~~~~ In file included from ../pbdata/FASTASequence.hpp:13, from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ 51 | DNASequence &operator=(const DNASequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/alloc_traits.h:33, from /usr/include/c++/11/ext/alloc_traits.h:34, from /usr/include/c++/11/bits/basic_string.h:40, from /usr/include/c++/11/string:55, from ../pbdata/FASTAReader.hpp:5, from ../pbdata/BlasrFASTAReader.cpp:2: /usr/include/c++/11/bits/stl_construct.h:109:7: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [128/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp [129/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o -c ../pbdata/GFFFile.cpp [130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o -c ../pbdata/MD5Utils.cpp [131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o -MF libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o -c ../pbdata/NucConversion.cpp [132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp [133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp [134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp [135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp [137/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFAtom.hpp:9, from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [139/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: ../pbdata/SMRTSequence.cpp:354:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 354 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ ../pbdata/SMRTSequence.cpp:379:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 379 | for (auto subread : subreads) { | ^~~~~~~~ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ [140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [141/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o [142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFBasReader_gtest.cpp:33:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp [147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp [149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp [150/187] c++ -o libblasr.so.5.3.5 libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.5 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp [152/187] /usr/bin/meson --internal symbolextractor /<>/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu libblasr.so.5.3.5 libblasr.so.5.3.5 libblasr.so.5.3.5.p/libblasr.so.5.3.5.symbols [153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp [155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp [157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp [158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFRegionTableReader.hpp:7, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp [160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp [161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp [163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp [164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = CCSSequence]’ ../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../hdf/HDFCCSReader.hpp:93:57: required from ‘int HDFCCSReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ ../unittest/hdf/HDFCCSReader_gtest.cpp:39:5: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp [168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp [169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -c ../unittest/pbdata/reads/RegionTypeMap_gtest.cpp [171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp [172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp [173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp [174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp [175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp [177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const string&, const UInt&, DNALength, DNALength, const string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 66 | return smrt; | ^~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymerase_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:133:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:133:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 133 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletion_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:192:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:192:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 192 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp: In member function ‘virtual void SMRTSequenceTest_MadeFromSubreadsAsPolymeraseNoInsertionNoDeletionNoSubstitution_Test::TestBody()’: ../unittest/pbdata/SMRTSequence_gtest.cpp:246:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ ../unittest/pbdata/SMRTSequence_gtest.cpp:246:39: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 246 | read3.MadeFromSubreadsAsPolymerase({read1, read2}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from ../unittest/pbdata/SMRTSequence_gtest.cpp:24: ../pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/gtest/gtest.h:60, from ../unittest/pbdata/SMRTSequence_gtest.cpp:22: /usr/include/c++/11/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ [179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp [180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp [181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp [182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp [183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp [184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -c ../unittest/pbdata/DNASequence_gtest.cpp [187/187] c++ -o unittest/libblasr_unittest unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>/pbseqlib-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 '-Wl,-rpath,$ORIGIN/..' -Wl,-rpath-link,/<>/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/ -Wl,--start-group libblasr.so.5.3.5 /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbseqlib-5.3.5+dfsg' /usr/bin/make -k gtest make[2]: Entering directory '/<>/pbseqlib-5.3.5+dfsg' make[2]: *** No rule to make target 'gtest'. make[2]: Leaving directory '/<>/pbseqlib-5.3.5+dfsg' make[1]: [debian/rules:31: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/<>/pbseqlib-5.3.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && DESTDIR=/<>/pbseqlib-5.3.5\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing libblasr.so.5.3.5 to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing libblasr.a to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing /<>/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/LibBlasrConfig.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr Installing /<>/pbseqlib-5.3.5+dfsg/hdf/BufferedHDF2DArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/BufferedHDF2DArrayImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/BufferedHDFArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/BufferedHDFArrayImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/DatasetCollection.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/DatasetCollectionImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDF2DArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFAlnGroupGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFAlnGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFAlnInfoGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFAtom.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFAttributable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFBaseCallsWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFBasReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFBasWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFBaxWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCCSReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpData.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpExperimentGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpRefAlignmentGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpRootGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCmpSupportedFields.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFCommonFG.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFConfig.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFData.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFFileLogGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFMovieInfoGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFNewBasReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFPlsReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFPlsWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFPulseCallsWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFPulseDataFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFPulseWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFRefGroupGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFRefInfoGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFRegionsWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFRegionTableReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFRegionTableWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFScanDataReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFScanDataWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFSentinalFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFSMRTSequenceReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFWriteBuffer.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFWriterBase.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFZMWMetricsWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFZMWReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/hdf/HDFZMWWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/hdf Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/FragmentSort.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPColumn.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPFragment.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPSet.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment/sdp Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AffineGuidedAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AffineKBandAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentFormats.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/BaseScoreFunction.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/ExtendAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/FullQVAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GraphPaper.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GraphPaperImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/GuidedAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/IDSScoreFunction.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/KBandAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/OneGapAlignment.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/QualityValueScoreFunction.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/ScoreMatrices.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SDPAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SDPAlignImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/StringToScoreMatrix.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SWAlign.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/alignment/SWAlignImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BasicEndpoint.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BasicEndpointImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BWTSearch.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/BWTSearchImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ClusterProbability.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/Coordinate.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/FindMaxInterval.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/GlobalChain.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/GlobalChainImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValue.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueWeightor.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISQValueWeightor.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISSizeWeightor.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/MapBySuffixArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/PrioritySearchTree.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ScoreAnchors.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/compare/CompareStrings.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/compare Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/DifferenceCovers.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/Karkkainen.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/LightweightSuffixArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/MultikeyQuicksort.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /<>/pbseqlib-5.3.5+dfsg/alignment/algorithms/sorting/qsufsort.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/algorithms/sorting Installing /<>/pbseqlib-5.3.5+dfsg/alignment/bwt/BWT.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /<>/pbseqlib-5.3.5+dfsg/alignment/bwt/Occ.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /<>/pbseqlib-5.3.5+dfsg/alignment/bwt/PackedHash.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /<>/pbseqlib-5.3.5+dfsg/alignment/bwt/Pos.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/bwt Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignedPair.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentCandidate.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentContext.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentGapList.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/Alignment.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentMap.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/AlignmentStats.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/ByteAlignment.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpIndexedStringTable.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpReadGroupTable.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/CmpRefSeqTable.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/FilterCriteria.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/Path.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignment Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/SAMQVConversion.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/alignmentset Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/AnchorParameters.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/ClusterList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/MatchPos.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/datastructures/anchoring/WeightedInterval.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/datastructures/anchoring Installing /<>/pbseqlib-5.3.5+dfsg/alignment/files/BaseSequenceIO.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /<>/pbseqlib-5.3.5+dfsg/alignment/files/CCSIterator.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /<>/pbseqlib-5.3.5+dfsg/alignment/files/FragmentCCSIterator.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /<>/pbseqlib-5.3.5+dfsg/alignment/files/ReaderAgglomerate.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /<>/pbseqlib-5.3.5+dfsg/alignment/files/ReaderAgglomerateImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/files Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/BAMPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/BAMPrinterImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/CompareSequencesPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/CompareSequencesPrinterImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/IntervalPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/SAMHeaderPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/SAMPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/SAMPrinterImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/StickAlignmentPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/SummaryPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/VulgarPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/format/XMLPrinter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/format Installing /<>/pbseqlib-5.3.5+dfsg/alignment/ipc/SharedMemoryAllocator.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/ipc Installing /<>/pbseqlib-5.3.5+dfsg/alignment/query/PbiFilterZmwGroupQuery.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /<>/pbseqlib-5.3.5+dfsg/alignment/query/SequentialZmwGroupQuery.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/query Installing /<>/pbseqlib-5.3.5+dfsg/alignment/qvs/QualityValueProfile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/qvs Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/CDFMap.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextOutputList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextSample.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/ContextSet.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/LengthHistogram.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSample.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSampleList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/OutputSampleListSet.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/simulator/QualitySample.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/simulator Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/AnchorDistributionTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/cdfs.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/LookupAnchorDistribution.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/pdfs.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/StatUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/StatUtilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/VarianceAccumulator.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/statistics/VarianceAccumulatorImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/statistics Installing /<>/pbseqlib-5.3.5+dfsg/alignment/suffixarray/LCPTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /<>/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SharedSuffixArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /<>/pbseqlib-5.3.5+dfsg/alignment/suffixarray/ssort.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /<>/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SuffixArray.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /<>/pbseqlib-5.3.5+dfsg/alignment/suffixarray/SuffixArrayTypes.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/suffixarray Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/BaseTuple.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/CompressedDNATuple.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/CountedTuple.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATuple.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATupleImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/DNATupleList.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/HashedTupleList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/HashedTupleListImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleCountTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleCountTableImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/tuple.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleList.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleListImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMask.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMatching.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMatchingImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleMetrics.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleOperations.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/tuples/TupleTranslations.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/tuples Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/FileOfFileNames.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/FileUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/LogUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/PhredUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/RangeUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/RegionUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/RegionUtilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/utils/SimpleXMLUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment/utils Installing /<>/pbseqlib-5.3.5+dfsg/alignment/MappingMetrics.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/alignment Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/alignment/CmpAlignment.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/alignment/CmpAlignmentImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/alignment Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/amos/AfgBasWriter.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/amos Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/loadpulses/MetricField.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/loadpulses Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/matrix/FlatMatrix.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/matrix/FlatMatrixImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/matrix/Matrix.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/matrix/MatrixImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/matrix Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/metagenome/FindRandomSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/metagenome/SequenceIndexDatabase.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/metagenome/TitleTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/metagenome Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityTransform.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValue.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVector.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityTransform.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValue.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVector.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/qvs/QualityValueVectorImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/qvs Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/AcqParams.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/BaseFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/BaseFileImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/HoleXY.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseBaseCommon.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/PulseFileImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/ReadInterval.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/ReadType.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionAnnotation.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionAnnotations.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionTable.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/RegionTypeMap.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/ScanData.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/reads/ZMWGroupEntry.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/reads Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/saf/AlnGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/saf/AlnInfo.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/saf/MovieInfo.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/saf/RefGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/saf/RefInfo.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/saf Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/AlignmentSet.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/AlignmentSetImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/CigarString.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/ReadGroup.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/ReferenceSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMAlignment.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMFlag.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMHeader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMKeywordValuePair.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMKeywordValuePairImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/sam/SAMReaderImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/sam Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utils/BitUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utils/SMRTReadUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utils/SMRTTitle.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utils/TimeUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata/utils Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/CCSSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/ChangeListID.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/CommandLineParser.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/Compare4BitCompressed.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/CompressedDNASequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/CompressedSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/CompressedSequenceImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/defs.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/DNASequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/Enumerations.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/FASTAReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/FASTASequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/FASTQReader.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/FASTQSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/GFFFile.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/MD5Utils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/MD5UtilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/NucConversion.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/PacBioDefs.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/PackedDNASequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/PrettyException.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/ReverseCompressIndex.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/SeqUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/SeqUtilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/SMRTSequence.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/StringUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/Types.h to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/utilsImpl.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/pbdata/VectorUtils.hpp to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/include/libblasr/pbdata Installing /<>/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu/meson-private/libblasr.pc to /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/<>/pbseqlib-5.3.5+dfsg' dh_install -p libpbdata-dev usr/include/libblasr/pbdata usr/include/pbseq dh_install -p libpbihdf-dev usr/include/libblasr/hdf usr/include/pbseq dh_install -p libblasr-dev usr/include/libblasr/alignment usr/include/pbseq find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete find debian/*/usr/include/ -name "*.mk" -delete d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libhdf5_serial_cpp103-dev/libhdf5-dev/ \ --override s/libpbbam1.6.0-dev/libpbbam-dev/ \ --override s/libpbcopper1.8.0-dev/libpbcopper-dev/ \ --movedev debian/tmp/usr/include/libblasr usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/x86_64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/libblasr.so Library package automatic movement utility --> libhdf5-dev package exists. --> libpbbam-dev package exists. --> libpbcopper-dev package exists. set -e install -d -m 755 debian/libblasr-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libblasr5.3.5/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.a debian/libblasr-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so debian/libblasr-dev/usr/lib/x86_64-linux-gnu mv /<>/pbseqlib-5.3.5+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libblasr.so.5.3.5 debian/libblasr5.3.5/usr/lib/x86_64-linux-gnu PKGDEV=libblasr-dev PKGSHL=libblasr5.3.5 install -d -m 755 debian/libblasr-dev/usr/include mv debian/tmp/usr/include/libblasr debian/libblasr-dev/usr/include install -d -m 755 debian/libblasr-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libblasr-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/libblasr-dev/usr/include/libblasr debian/libblasr-dev/usr/include/pbseq mv debian/libblasr-dev/usr/include/pbseq/libblasr/LibBlasrConfig.h debian/libblasr-dev/usr/include/pbseq dh_install make[1]: Leaving directory '/<>/pbseqlib-5.3.5+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a 17e213f1fb40d2f019efbc23b6b3d4c99f37af90 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libblasr-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libblasr-dev (in debian/libblasr-dev); do_strip: , oemstrip: pkgstriptranslations: processing libpbihdf-dev (in debian/libpbihdf-dev); do_strip: , oemstrip: pkgstriptranslations: processing libblasr5.3.5-dbgsym (in debian/.debhelper/libblasr5.3.5/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libpbseq-dev (in debian/libpbseq-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libblasr-dev/DEBIAN/control, package libblasr-dev, directory debian/libblasr-dev Searching for duplicated docs in dependency libblasr5.3.5... pkgstripfiles: processing control file: debian/libpbihdf-dev/DEBIAN/control, package libpbihdf-dev, directory debian/libpbihdf-dev symlinking changelog.Debian.gz in libblasr-dev to file in libblasr5.3.5 INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... Searching for duplicated docs in dependency libpbdata-dev... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libblasr-dev ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/libpbseq-dev/DEBIAN/control, package libpbseq-dev, directory debian/libpbseq-dev dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-2build1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libblasr5.3.5 (in debian/libblasr5.3.5); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libblasr5.3.5/DEBIAN/control, package libblasr5.3.5, directory debian/libblasr5.3.5 pkgstripfiles: Truncating usr/share/doc/libblasr5.3.5/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libblasr5.3.5 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-2build1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/libblasr5.3.5/dbgsym-root/DEBIAN/control, package libblasr5.3.5-dbgsym, directory debian/.debhelper/libblasr5.3.5/dbgsym-root dpkg-deb: building package 'libblasr5.3.5-dbgsym' in 'debian/.debhelper/scratch-space/build-libblasr5.3.5/libblasr5.3.5-dbgsym_5.3.5+dfsg-2build1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... INFO: pkgstripfiles: waiting for lock (libpbseq-dev) ... Renaming libblasr5.3.5-dbgsym_5.3.5+dfsg-2build1_amd64.deb to libblasr5.3.5-dbgsym_5.3.5+dfsg-2build1_amd64.ddeb INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libpbseq (in debian/libpbseq); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libpbseq/DEBIAN/control, package libpbseq, directory debian/libpbseq Searching for duplicated docs in dependency libblasr5.3.5... symlinking changelog.Debian.gz in libpbseq to file in libblasr5.3.5 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbseq ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-2build1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libpbihdf-dev) ... Searching for duplicated docs in dependency libpbdata-dev... symlinking changelog.Debian.gz in libpbseq-dev to file in libpbdata-dev Searching for duplicated docs in dependency libpbihdf-dev... Searching for duplicated docs in dependency libblasr-dev... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbseq-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-2build1_amd64.deb'. INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libpbdata-dev (in debian/libpbdata-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libpbdata-dev/DEBIAN/control, package libpbdata-dev, directory debian/libpbdata-dev pkgstripfiles: Truncating usr/share/doc/libpbdata-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbdata-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-2build1_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/libpbihdf-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbihdf-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-2build1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../pbseqlib_5.3.5+dfsg-2build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-12-10T17:16:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ pbseqlib_5.3.5+dfsg-2build1_amd64.changes: ------------------------------------------ Format: 1.8 Date: Fri, 10 Dec 2021 17:12:47 +0000 Source: pbseqlib Binary: libblasr-dev libblasr5.3.5 libpbdata-dev libpbihdf-dev libpbseq libpbseq-dev Built-For-Profiles: noudeb Architecture: amd64 Version: 5.3.5+dfsg-2build1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: libblasr-dev - tools for aligning PacBio reads to target sequences (development libblasr5.3.5 - tools for aligning PacBio reads to target sequences libpbdata-dev - tools for handling PacBio sequences (development files) libpbihdf-dev - tools for handling PacBio hdf5 files (development files) libpbseq - library for analyzing PacBio sequencing data libpbseq-dev - library for analyzing PacBio sequencing data (development files) Changes: pbseqlib (5.3.5+dfsg-2build1) jammy; urgency=medium . * No-change rebuild against libpbcopper1.9.3 Checksums-Sha1: 020a62ca17f884b639f05f34c5f61b0ebc9abb02 2444520 libblasr-dev_5.3.5+dfsg-2build1_amd64.deb e3aba914edafa66418bdb3624032599e43cda6c3 6870152 libblasr5.3.5-dbgsym_5.3.5+dfsg-2build1_amd64.ddeb 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procps (= 2:3.3.17-5ubuntu3), python3 (= 3.9.7-4), python3-distutils (= 3.9.9-3), python3-lib2to3 (= 3.9.9-3), python3-minimal (= 3.9.7-4), python3-pkg-resources (= 59.4.0-1), python3.9 (= 3.9.9-1build1), python3.9-minimal (= 3.9.9-1build1), readline-common (= 8.1-2build1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), tzdata (= 2021e-1ubuntu1), ubuntu-keyring (= 2021.03.26), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1639156367" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libblasr-dev_5.3.5+dfsg-2build1_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 2444520 bytes: control archive=9639 bytes. 913 bytes, 21 lines control 45335 bytes, 466 lines md5sums Package: libblasr-dev Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 15516 Depends: libblasr5.3.5 (= 5.3.5+dfsg-2build1), libpbdata-dev (= 5.3.5+dfsg-2build1) Breaks: libblasr (<< 5.3.3) Replaces: libblasr (<< 5.3.3) Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: tools for aligning PacBio reads to target sequences (development files) Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This package contains the header files and static library for the alignment sublibrary. 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./usr/share/doc/libblasr-dev/ lrwxrwxrwx root/root 0 2021-12-10 17:12 ./usr/share/doc/libblasr-dev/changelog.Debian.gz -> ../libblasr5.3.5/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libblasr-dev/copyright libblasr5.3.5_5.3.5+dfsg-2build1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 1274784 bytes: control archive=899 bytes. 882 bytes, 18 lines control 231 bytes, 3 lines md5sums 45 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libblasr5.3.5 Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 3038 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.4), libhdf5-103-1, libhdf5-cpp-103-1 (>= 1.10.5), libpbbam1.6.0 (>= 1.6.0+dfsg), libpbcopper1.9.3 (>= 1.9.3+dfsg), libstdc++6 (>= 11) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: tools for aligning PacBio reads to target sequences Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This package contains the alignment sublibrary. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-10 17:12 ./ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/lib/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 3092192 2021-12-10 17:12 ./usr/lib/x86_64-linux-gnu/libblasr.so.5.3.5 drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/libblasr5.3.5/ -rw-r--r-- root/root 1118 2021-12-10 17:12 ./usr/share/doc/libblasr5.3.5/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libblasr5.3.5/copyright libpbdata-dev_5.3.5+dfsg-2build1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 40818 bytes: control archive=3018 bytes. 759 bytes, 18 lines control 6805 bytes, 85 lines md5sums Package: libpbdata-dev Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 228 Depends: libpbcopper-dev Section: libdevel Priority: optional Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: tools for handling PacBio sequences (development files) Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This package contains the header files and static library for the pbdata sublibrary. 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./usr/share/doc/libpbdata-dev/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libpbdata-dev/copyright libpbihdf-dev_5.3.5+dfsg-2build1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 47298 bytes: control archive=2124 bytes. 753 bytes, 18 lines control 4158 bytes, 55 lines md5sums Package: libpbihdf-dev Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 330 Depends: libhdf5-dev Section: libdevel Priority: optional Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: tools for handling PacBio hdf5 files (development files) Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This package contains the header files and static library for the hdf sublibrary. 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0 2021-12-10 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/libpbihdf-dev/ -rw-r--r-- root/root 1117 2021-12-10 17:12 ./usr/share/doc/libpbihdf-dev/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libpbihdf-dev/copyright libpbseq-dev_5.3.5+dfsg-2build1_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 3082 bytes: control archive=664 bytes. 873 bytes, 18 lines control 71 bytes, 1 lines md5sums Package: libpbseq-dev Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 14 Depends: libpbdata-dev (= 5.3.5+dfsg-2build1), libpbihdf-dev (= 5.3.5+dfsg-2build1), libblasr-dev (= 5.3.5+dfsg-2build1) Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: library for analyzing PacBio sequencing data (development files) Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This is a metapackage that depends on the pbseqlib component development files. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-10 17:12 ./ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/libpbseq-dev/ lrwxrwxrwx root/root 0 2021-12-10 17:12 ./usr/share/doc/libpbseq-dev/changelog.Debian.gz -> ../libpbdata-dev/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libpbseq-dev/copyright libpbseq_5.3.5+dfsg-2build1_amd64.deb ------------------------------------- new Debian package, version 2.0. size 3062 bytes: control archive=640 bytes. 772 bytes, 18 lines control 67 bytes, 1 lines md5sums Package: libpbseq Source: pbseqlib Version: 5.3.5+dfsg-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 14 Depends: libblasr5.3.5 (= 5.3.5+dfsg-2build1) Section: science Priority: optional Multi-Arch: same Homepage: https://github.com/PacificBiosciences/blasr_libcpp Description: library for analyzing PacBio sequencing data Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment. . This is a metapackage that depends on the pbseqlib component shared libraries. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-10 17:12 ./ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/libpbseq/ lrwxrwxrwx root/root 0 2021-12-10 17:12 ./usr/share/doc/libpbseq/changelog.Debian.gz -> ../libblasr5.3.5/changelog.Debian.gz -rw-r--r-- root/root 4767 2021-10-08 11:50 ./usr/share/doc/libpbseq/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 93 Distribution: jammy-proposed Host Architecture: amd64 Install-Time: 13 Job: pbseqlib_5.3.5+dfsg-2build1.dsc Machine Architecture: amd64 Package: pbseqlib Package-Time: 106 Source-Version: 5.3.5+dfsg-2build1 Space: n/a Status: successful Version: 5.3.5+dfsg-2build1 -------------------------------------------------------------------------------- Finished at 2021-12-10T17:16:05Z Build needed 00:01:46, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22612920 Scanning for processes to kill in build PACKAGEBUILD-22612920