https://launchpad.net/ubuntu/+source/blasr/5.3.5+dfsg-1build2/+build/22612909 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-025 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 aarch64 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 17:14:37 ntpdate[1776]: adjust time server 10.211.37.1 offset -0.006058 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22612909 --image-type chroot /home/buildd/filecache-default/d7d0133902b8cc1df688a841d4b96e994eeac2e0 Creating target for build PACKAGEBUILD-22612909 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22612909 Starting target for build PACKAGEBUILD-22612909 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22612909 '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-22612909 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22612909 Updating target for build PACKAGEBUILD-22612909 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 arm64 Packages [1369 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe arm64 Packages [13.1 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5552 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 Packages [118 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [46.7 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 Packages [625 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 22.2 MB in 9s (2411 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-aarch64-linux-gnu binutils-common 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 libhwasan0 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 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 82.7 MB of archives. After this operation, 379 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main arm64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam0g arm64 1.4.0-10ubuntu2 [61.3 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt-dev arm64 1:4.4.26-1 [119 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt1 arm64 1:4.4.26-1 [87.0 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 base-files arm64 12ubuntu2 [63.2 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main arm64 debianutils arm64 5.5-1ubuntu1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 bash arm64 5.1-5ubuntu1 [771 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 bsdutils arm64 1:2.37.2-4ubuntu1 [84.5 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 libgpg-error0 arm64 1.42-3 [67.7 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcrypt20 arm64 1.9.4-3ubuntu2 [456 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 bzip2 arm64 1.0.8-5 [34.5 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libbz2-1.0 arm64 1.0.8-5 [36.0 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main arm64 libcc1-0 arm64 11.2.0-12ubuntu1 [54.1 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main arm64 gcc-11-base arm64 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcc-s1 arm64 11.2.0-12ubuntu1 [39.3 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 libgomp1 arm64 11.2.0-12ubuntu1 [115 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main arm64 libitm1 arm64 11.2.0-12ubuntu1 [28.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 libatomic1 arm64 11.2.0-12ubuntu1 [10.8 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 libasan6 arm64 11.2.0-12ubuntu1 [2228 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 liblsan0 arm64 11.2.0-12ubuntu1 [942 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main arm64 libtsan0 arm64 11.2.0-12ubuntu1 [2232 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main arm64 libubsan1 arm64 11.2.0-12ubuntu1 [908 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 libhwasan0 arm64 11.2.0-12ubuntu1 [1010 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 g++-11 arm64 11.2.0-12ubuntu1 [11.1 MB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 libstdc++-11-dev arm64 11.2.0-12ubuntu1 [2099 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcc-11-dev arm64 11.2.0-12ubuntu1 [1150 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 gcc-11 arm64 11.2.0-12ubuntu1 [19.4 MB] Get:28 http://ftpmaster.internal/ubuntu jammy/main arm64 cpp-11 arm64 11.2.0-12ubuntu1 [9734 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 libstdc++6 arm64 11.2.0-12ubuntu1 [623 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main arm64 libisl23 arm64 0.24-2 [690 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpc3 arm64 1.2.1-1 [48.1 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 libzstd1 arm64 1.4.8+dfsg-3 [311 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main arm64 libctf0 arm64 2.37-10ubuntu1 [102 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main arm64 libctf-nobfd0 arm64 2.37-10ubuntu1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main arm64 libbinutils arm64 2.37-10ubuntu1 [733 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main arm64 binutils-common arm64 2.37-10ubuntu1 [213 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main arm64 binutils arm64 2.37-10ubuntu1 [3160 B] Get:38 http://ftpmaster.internal/ubuntu jammy/main arm64 binutils-aarch64-linux-gnu arm64 2.37-10ubuntu1 [3214 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libssl3 arm64 3.0.0-1ubuntu2 [1752 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main arm64 libblkid1 arm64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 libuuid1 arm64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main arm64 libcryptsetup12 arm64 2:2.4.2-1ubuntu4 [205 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main arm64 libidn2-0 arm64 2.3.2-2 [67.1 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main arm64 libp11-kit0 arm64 0.24.0-6 [231 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main arm64 libtasn1-6 arm64 4.18.0-4 [42.6 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 libgnutls30 arm64 3.7.2-2ubuntu1 [917 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd-sysv arm64 249.5-2ubuntu2 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd-timesyncd arm64 249.5-2ubuntu2 [29.6 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libapparmor1 arm64 3.0.3-0ubuntu5 [37.7 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main arm64 libip4tc2 arm64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main arm64 libkmod2 arm64 28-1ubuntu5 [46.4 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main arm64 libpcre2-8-0 arm64 10.39-3 [201 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libselinux1 arm64 3.3-1build1 [74.3 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main arm64 libmount1 arm64 2.37.2-4ubuntu1 [120 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 libseccomp2 arm64 2.5.2-2ubuntu2 [47.9 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main arm64 login arm64 1:4.8.1-2ubuntu1 [186 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main arm64 util-linux arm64 2.37.2-4ubuntu1 [1059 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main arm64 mount arm64 2.37.2-4ubuntu1 [113 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd arm64 249.5-2ubuntu2 [4380 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsystemd0 arm64 249.5-2ubuntu2 [315 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libudev1 arm64 249.5-2ubuntu2 [75.5 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main arm64 libapt-pkg6.0 arm64 2.3.13 [864 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main arm64 dpkg arm64 1.20.9ubuntu3 [1244 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main arm64 dash arm64 0.5.11+git20210903+057cd650a4ed-3 [91.7 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main arm64 grep arm64 3.7-1 [152 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main arm64 libncurses6 arm64 6.3-1 [108 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main arm64 libncursesw6 arm64 6.3-1 [142 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main arm64 libtinfo6 arm64 6.3-1 [104 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-bin arm64 6.3-1 [183 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 sed arm64 4.8-1 [186 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 init-system-helpers all 1.61 [39.3 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-base all 6.3-1 [19.9 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main arm64 gpgv arm64 2.2.27-2ubuntu1 [133 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main arm64 apt arm64 2.3.13 [1353 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main arm64 libsepol2 arm64 3.3-1 [274 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:77 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsemanage2 arm64 3.3-1build1 [89.4 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main arm64 passwd arm64 1:4.8.1-2ubuntu1 [761 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam-modules-bin arm64 1.4.0-10ubuntu2 [38.6 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam-modules arm64 1.4.0-10ubuntu2 [278 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main arm64 logsave arm64 1.46.4-1ubuntu1 [10.7 kB] Get:82 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Setting up libasan6:arm64 (11.2.0-12ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 10 17:15:57 UTC 2021. Universal Time is now: Fri Dec 10 17:15:57 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:arm64 (6.3-1) ... Setting up libmpc3:arm64 (1.2.1-1) ... Setting up systemd-timesyncd (249.5-2ubuntu2) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:arm64 (11.2.0-12ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:arm64 (1.46.4-1ubuntu1) ... Setting up libncursesw6:arm64 (6.3-1) ... Setting up libdpkg-perl (1.20.9ubuntu3) ... Setting up logsave (1.46.4-1ubuntu1) ... Setting up libubsan1:arm64 (11.2.0-12ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libhwasan0:arm64 (11.2.0-12ubuntu1) ... Setting up libcrypt-dev:arm64 (1:4.4.26-1) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libbinutils:arm64 (2.37-10ubuntu1) ... Setting up libisl23:arm64 (0.24-2) ... Setting up openssl (3.0.0-1ubuntu2) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libcc1-0:arm64 (11.2.0-12ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up liblsan0:arm64 (11.2.0-12ubuntu1) ... Setting up libitm1:arm64 (11.2.0-12ubuntu1) ... Setting up libgdbm6:arm64 (1.22-1) ... Setting up libtsan0:arm64 (11.2.0-12ubuntu1) ... Setting up libctf0:arm64 (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 binutils-aarch64-linux-gnu (2.37-10ubuntu1) ... Setting up e2fsprogs (1.46.4-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... 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:arm64 (1.22-1) ... Setting up libgcc-11-dev:arm64 (11.2.0-12ubuntu1) ... Setting up gcc-11 (11.2.0-12ubuntu1) ... Setting up libstdc++-11-dev:arm64 (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-22612909 arm64 jammy-proposed -c chroot:build-PACKAGEBUILD-22612909 --arch=arm64 --dist=jammy-proposed --nolog blasr_5.3.5+dfsg-1build2.dsc Initiating build PACKAGEBUILD-22612909 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-025.buildd +==============================================================================+ | blasr 5.3.5+dfsg-1build2 (arm64) Fri, 10 Dec 2021 17:16:12 +0000 | +==============================================================================+ Package: blasr Version: 5.3.5+dfsg-1build2 Source Version: 5.3.5+dfsg-1build2 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22612909/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3.5+dfsg-1build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/blasr-mzoqPT/blasr-5.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-mzoqPT' 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-2Vi6sg/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-2Vi6sg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Vi6sg/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-2Vi6sg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Vi6sg/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-2Vi6sg/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (34.2 kB/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-2Vi6sg/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 (10.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13435 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.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 (arm64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~) Filtered Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~) dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<>/resolver-2Vi6sg/apt_archive/sbuild-build-depends-blasr-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-blasr-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-2Vi6sg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Vi6sg/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-2Vi6sg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Vi6sg/apt_archive ./ Sources [583 B] Get:5 copy:/<>/resolver-2Vi6sg/apt_archive ./ Packages [665 B] Fetched 2211 B in 0s (40.4 kB/s) Reading package lists... Reading package lists... Install blasr 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 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 libblasr-dev libblasr5.3.5 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 libpbdata-dev libpbihdf-dev libpbseq-dev 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 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 libblasr-dev libblasr5.3.5 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 libpbdata-dev libpbihdf-dev libpbseq-dev 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-blasr-dummy zlib1g-dev 0 upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 65.2 MB of archives. After this operation, 355 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2Vi6sg/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [754 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 libpython3.9-minimal arm64 3.9.9-1build1 [787 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main arm64 libexpat1 arm64 2.4.1-3 [75.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 python3.9-minimal arm64 3.9.9-1build1 [2128 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-minimal arm64 3.9.7-4 [24.7 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main arm64 media-types all 4.0.0 [22.2 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpdec3 arm64 2.5.1-2build1 [89.0 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 libpython3.9-stdlib arm64 3.9.9-1build1 [1803 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 python3.9 arm64 3.9.9-1build1 [437 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3-stdlib arm64 3.9.7-4 [7298 B] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3 arm64 3.9.7-4 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main arm64 bsdextrautils arm64 2.37.2-4ubuntu1 [70.1 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main arm64 libuchardet0 arm64 0.0.7-1build1 [76.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main arm64 groff-base arm64 1.22.4-7 [918 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main arm64 libpipeline1 arm64 1.5.4-1 [23.3 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 man-db arm64 2.9.4-2build1 [1175 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main arm64 libelf1 arm64 0.186-1 [51.1 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 libglib2.0-0 arm64 2.70.2-1 [1409 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 libicu67 arm64 67.1-7ubuntu1 [10.0 MB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 libxml2 arm64 2.9.12+dfsg-5 [725 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-pkg-resources all 59.4.0-1 [132 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic-mgc arm64 1:5.41-2 [257 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic1 arm64 1:5.41-2 [84.9 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 file arm64 1:5.41-2 [21.6 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext-base arm64 0.21-4ubuntu3 [35.2 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 libpsl5 arm64 0.21.0-1.2build1 [57.5 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 libuv1 arm64 1.42.0-1 [88.4 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main arm64 libsigsegv2 arm64 2.13-1ubuntu2 [14.5 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 m4 arm64 1.4.18-5ubuntu1 [196 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main arm64 autoconf all 2.71-2 [338 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main arm64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 automake all 1:1.16.5-1.1 [558 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main arm64 autopoint all 0.21-4ubuntu3 [422 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main arm64 libarchive13 arm64 3.4.3-2build1 [360 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main arm64 libbrotli1 arm64 1.0.9-2build4 [314 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg2-2build1 [21.2 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main arm64 libsasl2-2 arm64 2.1.27+dfsg2-2build1 [55.6 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main arm64 libldap-2.5-0 arm64 2.5.6+dfsg-1~exp1ubuntu1 [184 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libnghttp2-14 arm64 1.43.0-1build2 [75.3 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build3 [59.3 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 libssh-4 arm64 0.9.6-1build1 [183 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libcurl4 arm64 7.74.0-1.3ubuntu3 [269 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main arm64 libjsoncpp24 arm64 1.9.4-5 [76.8 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main arm64 librhash0 arm64 1.4.2-1 [125 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/universe arm64 dh-elpa-helper all 2.0.9ubuntu1 [7610 B] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 emacsen-common all 3.0.4 [14.9 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 cmake-data all 3.21.4-1ubuntu1 [1886 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 cmake arm64 3.21.4-1ubuntu1 [4625 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main arm64 libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main arm64 libtool all 2.4.6-15build1 [164 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main arm64 dh-autoreconf all 20 [16.1 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:54 http://ftpmaster.internal/ubuntu jammy/main arm64 libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:56 http://ftpmaster.internal/ubuntu jammy/main arm64 libdw1 arm64 0.186-1 [246 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main arm64 debugedit arm64 1:5.0-3 [46.3 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main arm64 dwz arm64 0.14-1build1 [102 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext arm64 0.21-4ubuntu3 [775 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main arm64 debhelper all 13.5.2ubuntu1 [926 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/universe arm64 googletest all 1.11.0-3 [541 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 hdf5-helpers arm64 1.10.7+repack-4ubuntu2 [14.2 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/universe arm64 libaec0 arm64 1.0.6-1 [19.5 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/universe arm64 libsz2 arm64 1.0.6-1 [5144 B] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-103-1 arm64 1.10.7+repack-4ubuntu2 [1207 kB] Get:68 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-cpp-103-1 arm64 1.10.7+repack-4ubuntu2 [121 kB] Get:69 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libcurl3-gnutls arm64 7.74.0-1.3ubuntu3 [264 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main arm64 libdeflate0 arm64 1.8-1ubuntu1 [53.2 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhtscodecs2 arm64 1.1.1-3 [55.8 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhts3 arm64 1.13+ds-2build1 [378 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbcopper1.8.0 arm64 1.8.0+dfsg-2 [371 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbbam1.6.0 arm64 1.6.0+dfsg-2 [594 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-2 [1248 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbcopper1.9.3 arm64 1.9.3+dfsg-2 [470 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbcopper-dev arm64 1.9.3+dfsg-2 [916 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbdata-dev arm64 5.3.5+dfsg-2 [40.8 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/universe arm64 libblasr-dev arm64 5.3.5+dfsg-2 [2432 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main arm64 libboost1.74-dev arm64 1.74.0-13ubuntu1 [9618 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main arm64 libboost-dev arm64 1.74.0.3ubuntu6 [3452 B] Get:82 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3ubuntu3 [366 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main arm64 libdeflate-dev arm64 1.8-1ubuntu1 [47.2 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main arm64 libgfortran5 arm64 11.2.0-12ubuntu1 [411 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/universe arm64 libgtest-dev arm64 1.11.0-3 [248 kB] Get:86 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-fortran-102 arm64 1.10.7+repack-4ubuntu2 [89.7 kB] Get:87 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-hl-100 arm64 1.10.7+repack-4ubuntu2 [58.4 kB] Get:88 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-hl-fortran-100 arm64 1.10.7+repack-4ubuntu2 [31.7 kB] Get:89 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-hl-cpp-100 arm64 1.10.7+repack-4ubuntu2 [10.4 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu7 [163 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main arm64 libjpeg-turbo8 arm64 2.1.1-0ubuntu1 [129 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main arm64 libjpeg-turbo8-dev arm64 2.1.1-0ubuntu1 [246 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:94 http://ftpmaster.internal/ubuntu jammy/main arm64 libjpeg8-dev arm64 8c-2ubuntu8 [1550 B] Get:95 http://ftpmaster.internal/ubuntu jammy/main arm64 libjpeg-dev arm64 8c-2ubuntu8 [1546 B] Get:96 http://ftpmaster.internal/ubuntu jammy/universe arm64 libaec-dev arm64 1.0.6-1 [17.5 kB] Get:97 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libssl-dev arm64 3.0.0-1ubuntu2 [2285 kB] Get:98 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 libhdf5-dev arm64 1.10.7+repack-4ubuntu2 [2941 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main arm64 liblzma-dev arm64 5.2.5-2build1 [159 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhts-dev arm64 1.13+ds-2build1 [5555 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbbam-dev arm64 1.6.0+dfsg-2 [75.5 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbihdf-dev arm64 5.3.5+dfsg-2 [47.3 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/universe arm64 libpbseq-dev arm64 5.3.5+dfsg-2 [3070 B] Get:104 http://ftpmaster.internal/ubuntu jammy/universe arm64 ninja-build arm64 1.10.1-1 [105 kB] Get:105 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-lib2to3 all 3.9.9-3 [77.7 kB] Get:106 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-distutils all 3.9.9-3 [144 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/universe arm64 meson all 0.60.2-1 [514 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main arm64 pkg-config arm64 0.29.2-1ubuntu2 [47.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 65.2 MB in 18s (3651 kB/s) Selecting previously unselected package libpython3.9-minimal:arm64. 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No schema files found: doing nothing. Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libbrotli1:arm64 (1.0.9-2build4) ... Setting up libnghttp2-14:arm64 (1.43.0-1build2) ... Setting up libmagic1:arm64 (1:5.41-2) ... Setting up libdeflate0:arm64 (1.8-1ubuntu1) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.41-2) ... Setting up googletest (1.11.0-3) ... Setting up libaec0:arm64 (1.0.6-1) ... Setting up ninja-build (1.10.1-1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg2-2build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:arm64 (1.42.0-1) ... Setting up emacsen-common (3.0.4) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build3) ... Setting up dh-elpa-helper (2.0.9ubuntu1) ... Setting up libsigsegv2:arm64 (2.13-1ubuntu2) ... Setting up libssl-dev:arm64 (3.0.0-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up pkg-config (0.29.2-1ubuntu2) ... Setting up libjpeg-turbo8:arm64 (2.1.1-0ubuntu1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg2-2build1) ... Setting up libssh-4:arm64 (0.9.6-1build1) ... Setting up libgfortran5:arm64 (11.2.0-12ubuntu1) ... Setting up libjsoncpp24:arm64 (1.9.4-5) ... Setting up liblzma-dev:arm64 (5.2.5-2build1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu7) ... Setting up librhash0:arm64 (1.4.2-1) ... Setting up libuchardet0:arm64 (0.0.7-1build1) ... Setting up libmpdec3:arm64 (2.5.1-2build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libpbcopper1.8.0:arm64 (1.8.0+dfsg-2) ... Setting up cmake-data (3.21.4-1ubuntu1) ... Setting up libboost-dev:arm64 (1.74.0.3ubuntu6) ... Setting up libpbcopper1.9.3:arm64 (1.9.3+dfsg-2) ... Setting up libdeflate-dev:arm64 (1.8-1ubuntu1) ... Setting up libelf1:arm64 (0.186-1) ... Setting up libxml2:arm64 (2.9.12+dfsg-5) ... Setting up libsz2:arm64 (1.0.6-1) ... Setting up libpython3.9-stdlib:arm64 (3.9.9-1build1) ... 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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:arm64 (8c-2ubuntu8) ... Setting up libpbdata-dev (5.3.5+dfsg-2) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3ubuntu3) ... Setting up python3 (3.9.7-4) ... Setting up libcurl4-gnutls-dev:arm64 (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:arm64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-cpp-103-1:arm64 (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:arm64 (1.10.7+repack-4ubuntu2) ... Setting up python3-pkg-resources (59.4.0-1) ... Setting up python3-distutils (3.9.9-3) ... Setting up libhts3:arm64 (1.13+ds-2build1) ... Setting up libhts-dev:arm64 (1.13+ds-2build1) ... Setting up meson (0.60.2-1) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-fortran-102:arm64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.7+repack-4ubuntu2) ... Setting up libpbbam1.6.0:arm64 (1.6.0+dfsg-2) ... Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-2) ... Setting up libblasr-dev:arm64 (5.3.5+dfsg-2) ... Setting up libhdf5-dev (1.10.7+repack-4ubuntu2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libpbbam-dev (1.6.0+dfsg-2) ... Setting up libpbihdf-dev (5.3.5+dfsg-2) ... Setting up libpbseq-dev:arm64 (5.3.5+dfsg-2) ... Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic arm64 (aarch64) 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-aarch64-linux-gnu_2.37-10ubuntu1 binutils-common_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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zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Dec 10 17:12:24 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 ./blasr_5.3.5+dfsg-1build2.dsc dpkg-source: info: extracting blasr in /<>/blasr-5.3.5+dfsg dpkg-source: info: unpacking blasr_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.5+dfsg-1build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch dpkg-source: info: applying 2to3.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-22612909 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22612909 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22612909 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-1build2 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary-arch dh binary-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/blasr-5.3.5+dfsg' LDFLAGS="-L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu -Dtests=false The Meson build system Version: 0.60.2 Source dir: /<>/blasr-5.3.5+dfsg Build dir: /<>/blasr-5.3.5+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: blasr 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: aarch64 Host machine cpu: aarch64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.5 Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.13+ds Library pbcopper found: YES Configuring BlasrVersion.h using configuration Program /usr/bin/meson found: YES (/usr/bin/meson) Build targets in project: 5 blasr 5.3.5 User defined options buildtype : plain libdir : lib/aarch64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload tests : false Found ninja-1.10.1 at /usr/bin/ninja make[1]: Leaving directory '/<>/blasr-5.3.5+dfsg' dh_auto_build -a -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<>/blasr-5.3.5+dfsg @BLASR_GIT_SHA1@ '(.*)' /<>/blasr-5.3.5+dfsg/git describe --always '--dirty=*' [2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 192 | charCount[0]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here 193 | case 0: //A | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 194 | charCount[1]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here 195 | case 1: //C | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 196 | charCount[2]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here 197 | case 2: //G | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 198 | charCount[3]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here 199 | case 3: //T | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 200 | charCount[4]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ [3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp [4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp [5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../extrautils/SWMatcher.cpp:2: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp [7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp [8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp [9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp [10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp [12/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../utils/SamToM4.cpp:19: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [13/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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/aarch64-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 /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [14/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../utils/SDPMatcher.cpp:3: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [15/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../utils/SamToCmpH5.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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp: In instantiation of ‘unsigned int AlignmentSetToCmpH5Adapter::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile >; std::string = std::__cxx11::basic_string]’: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:32: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidateList(std::vector >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ ../utils/SamToCmpH5.cpp:199:56: required from here /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:45: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); In file included from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ [16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp [17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../utils/SamFilter.cpp:29: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [18/25] c++ -Isawriter.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ sawriter.p/utils_SAWriter.cpp.o -MF sawriter.p/utils_SAWriter.cpp.o.d -o sawriter.p/utils_SAWriter.cpp.o -c ../utils/SAWriter.cpp [19/25] c++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp [20/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_LoadPulses.cpp.o -MF libblasr_impl.a.p/utils_LoadPulses.cpp.o.d -o libblasr_impl.a.p/utils_LoadPulses.cpp.o -c ../utils/LoadPulses.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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/aarch64-linux-gnu/c++/11/bits/c++allocator.h:33, from /usr/include/c++/11/bits/allocator.h:46, from /usr/include/c++/11/bits/stl_tree.h:64, from /usr/include/c++/11/map:60, from ../utils/LoadPulses.cpp:6: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [21/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o libblasr_impl.a.p/extrautils_SAModify.cpp.o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o libblasr_impl.a.p/extrautils_SALS.cpp.o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o libblasr_impl.a.p/extrautils_Evolve.cpp.o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o libblasr_impl.a.p/utils_SamToM4.cpp.o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o libblasr_impl.a.p/utils_SDPMatcher.cpp.o libblasr_impl.a.p/utils_LoadPulses.cpp.o libblasr_impl.a.p/utils_PulseToFasta.cpp.o libblasr_impl.a.p/utils_SamFilter.cpp.o [22/25] c++ -o sawriter sawriter.p/utils_SAWriter.cpp.o -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/aarch64-linux-gnu/libblasr.so /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/aarch64-linux-gnu/libblasr.so, may conflict with libpbcopper.so.1.9.3 [23/25] c++ -o toAfg toAfg.p/utils_ToAfg.cpp.o -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/aarch64-linux-gnu/libblasr.so /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/aarch64-linux-gnu/libpbbam.so, may conflict with libpbcopper.so.1.9.3 [24/25] c++ -Iblasr.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ blasr.p/Blasr.cpp.o -MF blasr.p/Blasr.cpp.o.d -o blasr.p/Blasr.cpp.o -c ../Blasr.cpp In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5, from ../Blasr.cpp:3: ../iblasr/BlasrMiscsImpl.hpp: In function ‘void MakeSubreadIntervals(std::vector&, std::vector&)’: ../iblasr/BlasrMiscsImpl.hpp:136:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 136 | for (auto subread : subreads) { | ^~~~~~~~ In file included from /usr/include/pbseq/pbdata/CCSSequence.hpp:5, from /usr/include/pbseq/alignment/files/CCSIterator.hpp:4, from ../iblasr/BlasrHeaders.h:57, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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 ../iblasr/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: ../iblasr/MappingParameters.h: In copy constructor ‘MappingParameters::MappingParameters(const MappingParameters&)’: ../iblasr/MappingParameters.h:19:7: warning: implicitly-declared ‘constexpr AnchorParameters::AnchorParameters(const AnchorParameters&)’ is deprecated [-Wdeprecated-copy] 19 | class MappingParameters | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:7, from ../iblasr/BlasrHeaders.h:42, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/anchoring/AnchorParameters.hpp:33:23: note: because ‘AnchorParameters’ has user-provided ‘AnchorParameters& AnchorParameters::operator=(const AnchorParameters&)’ 33 | AnchorParameters &operator=(const AnchorParameters &rhs); | ^~~~~~~~ ../Blasr.cpp: In function ‘void MapReadsNonCCS(MappingData >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector&, MappingParameters&, const int&, ReadAlignments&, std::ofstream&)’: ../Blasr.cpp:382:49: note: synthesized method ‘MappingParameters::MappingParameters(const MappingParameters&)’ first required here 382 | MappingParameters sensitiveParams = params; | ^~~~~~ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1407:32: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] 1407 | (void *(*)(void *))MapReads, &mapdb[procIndex]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:951:38: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 27 | if (dynamic_cast(&read) == NULL) { | ^ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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/aarch64-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 /usr/include/c++/11/iostream:39, from ../iblasr/BlasrHeaders.h:10, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:512:23: required from ‘int GuidedAlign(QSequence&, TSequence&, T_ScoreFn&, int, int, int, float, T_BufferCache&, blasr::Alignment&, AlignmentType, bool, int) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrAlignImpl.hpp:1449:20: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ In file included from /usr/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrUtilsImpl.hpp:639:19: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:689:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:698:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] In file included from /usr/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp: In instantiation of ‘int OneGapAlign(T_QuerySequence&, T_RefSequence&, T_ScoreFunction&, T_BufferList&, blasr::Alignment&) [with T_QuerySequence = FASTQSequence; T_RefSequence = DNASequence; T_ScoreFunction = DistanceMatrixScoreFunction; T_BufferList = MappingBuffers]’: ../iblasr/BlasrAlignImpl.hpp:918:40: required from ‘void AlignIntervals(T_TargetSequence&, T_QuerySequence&, T_QuerySequence&, WeightedIntervalSet&, int (*)[5], int, int, int, int, SequenceIndexDatabase&, std::vector*>&, MappingParameters&, MappingBuffers&, int) [with T_TargetSequence = FASTASequence; T_QuerySequence = SMRTSequence; TDBSequence = FASTQSequence]’ ../iblasr/BlasrAlignImpl.hpp:280:23: required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr&, T_TupleCountTable&, SequenceIndexDatabase&, MappingParameters&, MappingMetrics&, std::vector*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray >; T_TupleCountTable = TupleCountTable; BWT = Bwt; MappingIPC = MappingData >, FASTASequence, DNATuple>]’ ../Blasr.cpp:347:16: required from here /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp:337:40: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 337 | assert(distanceBetweenLeftAndRight >= 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1301:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1310:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: ../Blasr.cpp: In function ‘AlignmentToBamRecord(AlignmentCandidate&, SMRTSequence&, SMRTSequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool)void’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 27 | if (dynamic_cast(&read) == NULL) { | ^~ [25/25] c++ -o blasr blasr.p/Blasr.cpp.o -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/blasr-5.3.5+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/aarch64-linux-gnu/libblasr.so /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/aarch64-linux-gnu/libpbbam.so, may conflict with libpbcopper.so.1.9.3 debian/rules override_dh_auto_test make[1]: Entering directory '/<>/blasr-5.3.5+dfsg' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/<>/blasr-5.3.5+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson dh_prep -a -O--buildsystem=meson dh_auto_install --destdir=debian/blasr/ -a -O--buildsystem=meson cd obj-aarch64-linux-gnu && DESTDIR=/<>/blasr-5.3.5\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command [1/2] Installing files. Installing blasr to /<>/blasr-5.3.5+dfsg/debian/blasr/usr/bin Installing sawriter to /<>/blasr-5.3.5+dfsg/debian/blasr/usr/bin dh_install -a -O--buildsystem=meson dh_installdocs -a -O--buildsystem=meson dh_installchangelogs -a -O--buildsystem=meson dh_installexamples -a -O--buildsystem=meson dh_installman -a -O--buildsystem=meson dh_installsystemduser -a -O--buildsystem=meson dh_lintian -a -O--buildsystem=meson dh_perl -a -O--buildsystem=meson dh_link -a -O--buildsystem=meson dh_strip_nondeterminism -a -O--buildsystem=meson dh_compress -a -O--buildsystem=meson dh_fixperms -a -O--buildsystem=meson dh_missing -a -O--buildsystem=meson dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson debugedit: debian/blasr/usr/bin/blasr: Unknown DWARF DW_FORM_0x1f20 1fb03bdd17585f0471964514489ca3d8bccea700 debugedit: debian/blasr/usr/bin/sawriter: Unknown DWARF DW_FORM_0x1f20 2d809550320adae5e501eb116218e4571f32fc04 dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -a -O--buildsystem=meson dh_gencontrol -a -O--buildsystem=meson dh_md5sums -a -O--buildsystem=meson dh_builddeb -a -O--buildsystem=meson INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing blasr-dbgsym (in debian/.debhelper/blasr/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr pkgstripfiles: Truncating usr/share/doc/blasr/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package blasr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-1build2_arm64.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/blasr/dbgsym-root/DEBIAN/control, package blasr-dbgsym, directory debian/.debhelper/blasr/dbgsym-root dpkg-deb: building package 'blasr-dbgsym' in 'debian/.debhelper/scratch-space/build-blasr/blasr-dbgsym_5.3.5+dfsg-1build2_arm64.deb'. Renaming blasr-dbgsym_5.3.5+dfsg-1build2_arm64.deb to blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../blasr_5.3.5+dfsg-1build2_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-12-10T17:20:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-1build2_arm64.changes: --------------------------------------- Format: 1.8 Date: Fri, 10 Dec 2021 17:12:23 +0000 Source: blasr Binary: blasr Built-For-Profiles: noudeb Architecture: arm64 Version: 5.3.5+dfsg-1build2 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.5+dfsg-1build2) jammy; urgency=medium . * No-change rebuild against libpbcopper1.9.3 Checksums-Sha1: 8ee224bacdabe8ff459f722653a854ff898a14e7 2721006 blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 2ce1cebf9ead02df81b51728b1474300f758b3a5 8681 blasr_5.3.5+dfsg-1build2_arm64.buildinfo 8e7772f5038247b143eb010b67868bdeb9b60356 215154 blasr_5.3.5+dfsg-1build2_arm64.deb Checksums-Sha256: 5e28b415fdcc1ca4873e1997a91c77a0184ce5805691d4dee4714173fafa77c2 2721006 blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 4aba2d62a4a3270f3c54f580bacd1746291b0039588bd1a638dfd0e2b1abbaf7 8681 blasr_5.3.5+dfsg-1build2_arm64.buildinfo 33af7a6cb76f090795658248c42bbc6975c99ec28fd7c17fbe570cd14462d98d 215154 blasr_5.3.5+dfsg-1build2_arm64.deb Files: b3c4c807ce60fd7d7cb0934714d7a698 2721006 debug optional blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 961197be84d44367c1f7091125cf9357 8681 science optional blasr_5.3.5+dfsg-1build2_arm64.buildinfo 7130f62a51fd3a970441757fd6d39f4e 215154 science optional blasr_5.3.5+dfsg-1build2_arm64.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: blasr Binary: blasr blasr-dbgsym Architecture: arm64 Version: 5.3.5+dfsg-1build2 Checksums-Md5: b3c4c807ce60fd7d7cb0934714d7a698 2721006 blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 7130f62a51fd3a970441757fd6d39f4e 215154 blasr_5.3.5+dfsg-1build2_arm64.deb Checksums-Sha1: 8ee224bacdabe8ff459f722653a854ff898a14e7 2721006 blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 8e7772f5038247b143eb010b67868bdeb9b60356 215154 blasr_5.3.5+dfsg-1build2_arm64.deb Checksums-Sha256: 5e28b415fdcc1ca4873e1997a91c77a0184ce5805691d4dee4714173fafa77c2 2721006 blasr-dbgsym_5.3.5+dfsg-1build2_arm64.ddeb 33af7a6cb76f090795658248c42bbc6975c99ec28fd7c17fbe570cd14462d98d 215154 blasr_5.3.5+dfsg-1build2_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Fri, 10 Dec 2021 17:20:41 +0000 Build-Path: /<>/blasr-5.3.5+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: 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-aarch64-linux-gnu (= 2.37-10ubuntu1), binutils-common (= 2.37-10ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), cmake (= 3.21.4-1ubuntu1), cmake-data (= 3.21.4-1ubuntu1), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-12ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2ubuntu1), debianutils (= 5.5-1ubuntu1), debugedit (= 1:5.0-3), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9ubuntu1), dh-strip-nondeterminism (= 1.12.1-1), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu3), dpkg-dev (= 1.20.9ubuntu3), dwz (= 0.14-1build1), emacsen-common (= 3.0.4), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-12ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-12ubuntu1), gcc-11-base (= 11.2.0-12ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), googletest (= 1.11.0-3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hdf5-helpers (= 1.10.7+repack-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.61), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2build1), libasan6 (= 11.2.0-12ubuntu1), libatomic1 (= 11.2.0-12ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-10ubuntu1), libblasr-dev (= 5.3.5+dfsg-2), libblasr5.3.5 (= 5.3.5+dfsg-2), libblkid1 (= 2.37.2-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu6), libboost1.74-dev (= 1.74.0-13ubuntu1), libbrotli1 (= 1.0.9-2build4), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-12ubuntu1), libcom-err2 (= 1.46.4-1ubuntu1), libcrypt-dev (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-10ubuntu1), libctf0 (= 2.37-10ubuntu1), libcurl3-gnutls (= 7.74.0-1.3ubuntu3), libcurl4 (= 7.74.0-1.3ubuntu3), libcurl4-gnutls-dev (= 7.74.0-1.3ubuntu3), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.5.2ubuntu1), libdeflate-dev (= 1.8-1ubuntu1), libdeflate0 (= 1.8-1ubuntu1), libdpkg-perl (= 1.20.9ubuntu3), libdw1 (= 0.186-1), libelf1 (= 0.186-1), libexpat1 (= 2.4.1-3), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.1-1), libgcc-11-dev (= 11.2.0-12ubuntu1), libgcc-s1 (= 11.2.0-12ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgfortran5 (= 11.2.0-12ubuntu1), libglib2.0-0 (= 2.70.2-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.2-2ubuntu1), libgomp1 (= 11.2.0-12ubuntu1), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.19.2-0ubuntu1), libgtest-dev (= 1.11.0-3), libhdf5-103-1 (= 1.10.7+repack-4ubuntu2), libhdf5-cpp-103-1 (= 1.10.7+repack-4ubuntu2), libhdf5-dev (= 1.10.7+repack-4ubuntu2), libhdf5-fortran-102 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-100 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-cpp-100 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-fortran-100 (= 1.10.7+repack-4ubuntu2), libhogweed6 (= 3.7.3-1build1), libhts-dev (= 1.13+ds-2build1), libhts3 (= 1.13+ds-2build1), libhtscodecs2 (= 1.1.1-3), libhwasan0 (= 11.2.0-12ubuntu1), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-12ubuntu1), libjpeg-dev (= 8c-2ubuntu8), libjpeg-turbo8 (= 2.1.1-0ubuntu1), libjpeg-turbo8-dev (= 2.1.1-0ubuntu1), libjpeg8 (= 8c-2ubuntu8), libjpeg8-dev (= 8c-2ubuntu8), libjsoncpp24 (= 1.9.4-5), libk5crypto3 (= 1.19.2-0ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.19.2-0ubuntu1), libkrb5support0 (= 1.19.2-0ubuntu1), libldap-2.5-0 (= 2.5.6+dfsg-1~exp1ubuntu1), liblsan0 (= 11.2.0-12ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma-dev (= 5.2.5-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libncurses6 (= 6.3-1), libncursesw6 (= 6.3-1), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build2), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libp11-kit0 (= 0.24.0-6), libpam-modules (= 1.4.0-10ubuntu2), libpam-modules-bin (= 1.4.0-10ubuntu2), libpam-runtime (= 1.4.0-10ubuntu2), libpam0g (= 1.4.0-10ubuntu2), libpbbam-dev (= 1.6.0+dfsg-2), libpbbam1.6.0 (= 1.6.0+dfsg-2), libpbcopper-dev (= 1.9.3+dfsg-2), libpbcopper1.8.0 (= 1.8.0+dfsg-2), libpbcopper1.9.3 (= 1.9.3+dfsg-2), libpbdata-dev (= 5.3.5+dfsg-2), libpbihdf-dev (= 5.3.5+dfsg-2), libpbseq-dev (= 5.3.5+dfsg-2), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.4-1), libprocps8 (= 2:3.3.17-5ubuntu3), libpsl5 (= 0.21.0-1.2build1), libpython3-stdlib (= 3.9.7-4), libpython3.9-minimal (= 3.9.9-1build1), libpython3.9-stdlib (= 3.9.9-1build1), libreadline8 (= 8.1-2build1), librhash0 (= 1.4.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libsasl2-2 (= 2.1.27+dfsg2-2build1), libsasl2-modules-db (= 2.1.27+dfsg2-2build1), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libsqlite3-0 (= 3.36.0-2), libssh-4 (= 0.9.6-1build1), libssl-dev (= 3.0.0-1ubuntu2), libssl3 (= 3.0.0-1ubuntu2), libstdc++-11-dev (= 11.2.0-12ubuntu1), libstdc++6 (= 11.2.0-12ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.5-2ubuntu2), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-12ubuntu1), libubsan1 (= 11.2.0-12ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.5-2ubuntu2), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libuv1 (= 1.42.0-1), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-13.13), login (= 1:4.8.1-2ubuntu1), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 17), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), meson (= 0.60.2-1), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), ninja-build (= 1.10.1-1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), pkg-config (= 0.29.2-1ubuntu2), po-debconf (= 1.0.21+nmu1), 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), 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="1639156343" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-1build2_arm64.deb ---------------------------------- new Debian package, version 2.0. size 215154 bytes: control archive=1131 bytes. 874 bytes, 15 lines control 982 bytes, 15 lines md5sums Package: blasr Version: 5.3.5+dfsg-1build2 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 533 Depends: libblasr5.3.5 (>= 5.3.5+dfsg), libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libhdf5-cpp-103-1 (>= 1.10.5), libpbbam1.6.0 (>= 1.6.0+dfsg), libpbcopper1.9.3 (>= 1.9.3+dfsg), libstdc++6 (>= 11), libpbseq Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. 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/bin/ -rwxr-xr-x root/root 469272 2021-12-10 17:12 ./usr/bin/blasr -rwxr-xr-x root/root 43264 2021-12-10 17:12 ./usr/bin/sawriter 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/blasr/ -rw-r--r-- root/root 373 2021-10-11 08:14 ./usr/share/doc/blasr/NEWS.Debian.gz -rw-r--r-- root/root 1291 2021-02-18 10:03 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 208 2021-10-11 08:14 ./usr/share/doc/blasr/README.source -rw-r--r-- root/root 542 2021-10-11 08:14 ./usr/share/doc/blasr/README.test -rw-r--r-- root/root 41 2021-10-11 08:14 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 1198 2021-12-10 17:12 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2193 2021-10-11 08:14 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/doc/blasr/examples/ -rw-r--r-- root/root 65 2021-10-11 08:14 ./usr/share/doc/blasr/examples/query.fasta -rw-r--r-- root/root 72 2021-10-11 08:14 ./usr/share/doc/blasr/examples/ref.fa -rw-r--r-- root/root 897 2021-10-11 08:14 ./usr/share/doc/blasr/run-unit-test drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 84 2021-10-11 08:14 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/man/ drwxr-xr-x root/root 0 2021-12-10 17:12 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2021-12-10 17:12 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2021-12-10 17:12 ./usr/share/man/man1/sawriter.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 193 Distribution: jammy-proposed Host Architecture: arm64 Install-Time: 74 Job: blasr_5.3.5+dfsg-1build2.dsc Machine Architecture: arm64 Package: blasr Package-Time: 270 Source-Version: 5.3.5+dfsg-1build2 Space: n/a Status: successful Version: 5.3.5+dfsg-1build2 -------------------------------------------------------------------------------- Finished at 2021-12-10T17:20:42Z Build needed 00:04:30, 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=arm64 PACKAGEBUILD-22612909 Scanning for processes to kill in build PACKAGEBUILD-22612909