https://launchpad.net/ubuntu/+source/blasr/5.3.5+dfsg-6build4/+build/27790033 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-arm64-020 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 18 Feb 21:01:36 ntpdate[1877]: adjust time server 10.211.37.1 offset -0.000320 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27790033 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27790033 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27790033 Starting target for build PACKAGEBUILD-27790033 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27790033 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27790033 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27790033 Updating target for build PACKAGEBUILD-27790033 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1411 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.4 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6030 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [223 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [68.5 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [951 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [400 kB] Fetched 25.6 MB in 4s (7160 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils ca-certificates coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 156 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 120 MB of archives. After this operation, 76.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu1 [1596 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu1 [19.7 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-5build1 [139 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-5build1 [347 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-5build1 [85.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-5build1 [33.5 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3 [9550 B] Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3 arm64 3.0.10-1ubuntu4 [1764 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3 arm64 1.3.4+ds-1build1 [99.3 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3 [40.9 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6 arm64 2.39-0ubuntu1 [2764 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-bin arm64 2.39-0ubuntu1 [587 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-14-base arm64 14-20240201-3ubuntu1 [46.4 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-s1 arm64 14-20240201-3ubuntu1 [49.9 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu6 [84.1 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.16 [93.7 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu1 [777 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.2-6ubuntu1 [96.9 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 coreutils arm64 9.4-2ubuntu3 [1384 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.4.5-0.3 [140 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++6 arm64 14-20240201-3ubuntu1 [750 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.1-4ubuntu1 [19.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libapparmor1 arm64 4.0.0~alpha4-0ubuntu1 [49.4 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-2 [5594 B] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-2 [14.7 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-2 [47.4 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.2-6ubuntu1 [121 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 30+20230601-2ubuntu1 [49.8 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libselinux1 arm64 3.5-2build1 [79.5 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.2-6ubuntu1 [132 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.38 arm64 5.38.2-3 [4772 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 perl arm64 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 perl-base arm64 5.38.2-3 [1777 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblocale-gettext-perl arm64 1.07-6build1 [15.0 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-iconv-perl arm64 1.7-8build1 [13.0 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-charwidth-perl arm64 0.04-11build1 [9316 B] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.36 arm64 5.36.0-10ubuntu1 [4673 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3 arm64 5.3.28+dfsg2-4 [718 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6 arm64 1.23-5 [33.8 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4 arm64 1.23-5 [6302 B] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3ubuntu1 [61.6 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf-i18n all 1.5.86 [205 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf all 1.5.86 [124 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.2-9.1ubuntu2 [65.8 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libseccomp2 arm64 2.5.5-1ubuntu1 [51.0 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-sysv arm64 255.2-3ubuntu2 [11.9 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-dev all 255.2-3ubuntu2 [101 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 systemd arm64 255.2-3ubuntu2 [3397 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd-shared arm64 255.2-3ubuntu2 [2012 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.2-6ubuntu1 [34.3 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.6.1-6ubuntu1 [240 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.2-6ubuntu1 [141 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.2-6ubuntu1 [116 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd0 arm64 255.2-3ubuntu2 [421 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libudev1 arm64 255.2-3ubuntu2 [170 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libapt-pkg6.0 arm64 2.7.11 [930 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.4ubuntu3 [1268 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu1 [186 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.2-6ubuntu1 [1113 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu1 [11.2 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-3ubuntu1 [33.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 apt arm64 2.7.11 [1334 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 apt-utils arm64 2.7.11 [205 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgv arm64 2.4.4-2ubuntu3 [149 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.4-2 [22.2 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu1 [275 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2 [67.1 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libgnutls30 arm64 3.8.3-1ubuntu1 [942 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.2-9.1ubuntu2 [47.0 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.2-9.1ubuntu2 [284 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.2-6ubuntu1 [62.9 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.2-6ubuntu1 [32.3 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build2 [10.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build2 [90.9 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu1 [146 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu1 [104 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-3ubuntu1 [837 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-13ubuntu1 [14.0 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-13ubuntu1 [463 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-13ubuntu1 [1030 B] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [10.3 MB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240201-3ubuntu1 [44.8 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-2ubuntu1 [777 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-2ubuntu1 [95.7 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-2ubuntu1 [99.5 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-2ubuntu1 [14.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-2ubuntu1 [3294 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-2ubuntu1 [768 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-2ubuntu1 [18.1 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-2ubuntu1 [239 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-13ubuntu1 [2319 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240201-3ubuntu1 [144 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240201-3ubuntu1 [27.6 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240201-3ubuntu1 [11.4 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240201-3ubuntu1 [2919 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240201-3ubuntu1 [1281 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-13ubuntu1 [2463 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240201-3ubuntu1 [2689 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240201-3ubuntu1 [1150 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240201-3ubuntu1 [1597 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [20.1 MB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [11.7 MB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-13ubuntu1 [46.6 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-2ubuntu1 [56.5 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1 [124 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-2ubuntu1 [706 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 openssl arm64 3.0.10-1ubuntu4 [983 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu1 [23.3 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-3 [56.2 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8 arm64 8.2-3 [152 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 libsqlite3-0 arm64 3.45.1-1 [704 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-1ubuntu1 [273 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.2-6ubuntu1 [71.4 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16 arm64 1.6.42-1 [185 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 psmisc arm64 23.6-2 [178 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.4.5-0.3 [277 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:156 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.4ubuntu3 [1078 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.4ubuntu3 [268 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 46 [12.3 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu1 [34.0 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg arm64 2.4.4-2ubuntu3 [547 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgconf arm64 2.4.4-2ubuntu3 [102 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg-agent arm64 2.4.4-2ubuntu3 [221 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 optipng arm64 0.7.8+ds-1 [109 kB] Preconfiguring packages ... 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Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libgprofng0:arm64 (2.42-2ubuntu1) ... Setting up optipng (0.7.8+ds-1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-5build1) ... Setting up libgdbm-compat4:arm64 (1.23-5) ... Setting up libgcc-13-dev:arm64 (13.2.0-13ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu3) ... Setting up libperl5.36:arm64 (5.36.0-10ubuntu1) ... Setting up gpg (2.4.4-2ubuntu3) ... Setting up libtirpc3:arm64 (1.3.4+ds-1build1) ... Setting up gpg-agent (2.4.4-2ubuntu3) ... Setting up cpp-13 (13.2.0-13ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.42-2ubuntu1) ... Setting up libperl5.38:arm64 (5.38.2-3) ... Setting up binutils (2.42-2ubuntu1) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-13ubuntu1) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-13ubuntu1) ... Setting up libdpkg-perl (1.22.4ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up dpkg-dev (1.22.4ubuntu3) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.39-0ubuntu1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-13ubuntu1) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-13ubuntu1) ... Setting up g++-13 (13.2.0-13ubuntu1) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu1) ... Processing triggers for debianutils (5.16) ... Processing triggers for ca-certificates (20240203) ... 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-27790033 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27790033 --arch=arm64 --dist=noble-proposed --nolog blasr_5.3.5+dfsg-6build4.dsc Initiating build PACKAGEBUILD-27790033 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-arm64-020.buildd +==============================================================================+ | blasr 5.3.5+dfsg-6build4 (arm64) Sun, 18 Feb 2024 21:02:27 +0000 | +==============================================================================+ Package: blasr Version: 5.3.5+dfsg-6build4 Source Version: 5.3.5+dfsg-6build4 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27790033/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-7KrocP/resolver-Sz4vQ6' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3.5+dfsg-6build4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/blasr-7KrocP/blasr-5.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-7KrocP' with '<>' +------------------------------------------------------------------------------+ | 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-4~), build-essential, fakeroot 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-4~), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [458 B] Get:5 copy:/<>/apt_archive ./ Packages [545 B] Fetched 1960 B in 0s (22.8 kB/s) Reading package lists... Reading package lists... Install main 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: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz 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 libboost1.83-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 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 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam-dev libpbbam2.4.0 libpbcopper-dev libpbcopper2.3.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libgnutls28-dev libidn-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 python-setuptools-doc python3.12-venv python3.12-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz 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 libboost1.83-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 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 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam-dev libpbbam2.4.0 libpbcopper-dev libpbcopper2.3.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 79.0 MB of archives. After this operation, 408 MB of additional disk space will be used. 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ninja-build arm64 1.11.1-2 [125 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 meson all 1.3.2-1 [604 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] Preconfiguring packages ... Fetched 79.0 MB in 4s (21.7 MB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15839 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.0-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-1_arm64.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Setting up libpython3.12-minimal:arm64 (3.12.2-1) ... Setting up libexpat1:arm64 (2.6.0-1) ... Setting up python3.12-minimal (3.12.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16157 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_arm64.deb ... 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Setting up libhtscodecs2:arm64 (1.6.0-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libboost1.83-dev:arm64 (1.83.0-2ubuntu1) ... Setting up libpsl5:arm64 (0.21.2-1build1) ... Setting up hdf5-helpers (1.10.10+repack-3ubuntu1) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.13ubuntu1) ... Setting up libbrotli1:arm64 (1.1.0-2) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libmagic1:arm64 (1:5.45-2) ... Setting up libdeflate0:arm64 (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2) ... Setting up googletest (1.14.0-1) ... Setting up libaec0:arm64 (1.1.2-1) ... Setting up ninja-build (1.11.1-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-2) ... Setting up libuv1:arm64 (1.46.0-3ubuntu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libssl-dev:arm64 (3.0.10-1ubuntu4) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libjsoncpp25:arm64 (1.9.5-6) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4) ... Setting up libssh-4:arm64 (0.10.6-2) ... Setting up libgfortran5:arm64 (14-20240201-3ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:arm64 (5.4.5-0.3) ... Setting up libicu74:arm64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libuchardet0:arm64 (0.0.8-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up cmake-data (3.28.3-1) ... Setting up libboost-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libdeflate-dev:arm64 (1.19-1) ... Setting up libelf1:arm64 (0.190-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu1) ... Setting up libldap2:arm64 (2.6.7+dfsg-1~exp1ubuntu1) ... Setting up libsz2:arm64 (1.1.2-1) ... Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... Setting up libjpeg8:arm64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:arm64 (0.190-1) ... Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:arm64 (3.12.2-1) ... Setting up libgtest-dev:arm64 (1.14.0-1) ... Setting up libtool (2.4.7-7) ... Setting up libarchive13:arm64 (3.7.2-1ubuntu2) ... Setting up python3.12 (3.12.2-1) ... Setting up libaec-dev:arm64 (1.1.2-1) ... Setting up libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ... Setting up libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu2) ... Setting up pkgconf:arm64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.1-2) ... Setting up libpbcopper-dev:arm64 (2.3.0+dfsg-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:arm64 (8.5.0-2ubuntu2) ... Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... Setting up libpython3-stdlib:arm64 (3.12.1-0ubuntu1) ... Setting up libhts3:arm64 (1.19+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... Setting up libpbdata-dev:arm64 (5.3.5+dfsg-6build3) ... Setting up libhts-dev:arm64 (1.19+ds-1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu1) ... Setting up cmake (3.28.3-1) ... Setting up libpbbam-dev:arm64 (2.4.0+dfsg-1build1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up meson (1.3.2-1) ... Setting up debhelper (13.13ubuntu1) ... Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.10+repack-3ubuntu1) ... Setting up libhdf5-fortran-102:arm64 (1.10.10+repack-3ubuntu1) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.10+repack-3ubuntu1) ... Setting up libhdf5-dev (1.10.10+repack-3ubuntu1) ... 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 libpbihdf-dev:arm64 (5.3.5+dfsg-6build3) ... Setting up libblasr-dev:arm64 (5.3.5+dfsg-6build3) ... Setting up libpbseq-dev:arm64 (5.3.5+dfsg-6build3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.2-3ubuntu2) ... Processing triggers for libc-bin (2.39-0ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-2ubuntu1 dpkg-dev_1.22.4ubuntu3 g++-13_13.2.0-13ubuntu1 gcc-13_13.2.0-13ubuntu1 libc6-dev_2.39-0ubuntu1 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.11 apt-utils_2.7.11 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 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libboost1.83-dev_1.83.0-2ubuntu1 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.39-0ubuntu1 libc-dev-bin_2.39-0ubuntu1 libc6_2.39-0ubuntu1 libc6-dev_2.39-0ubuntu1 libcap-ng0_0.8.4-2 libcap2_1:2.66-4ubuntu1 libcc1-0_14-20240201-3ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.42-2ubuntu1 libctf0_2.42-2ubuntu1 libcurl3-gnutls_8.5.0-2ubuntu2 libcurl4_8.5.0-2ubuntu2 libcurl4-gnutls-dev_8.5.0-2ubuntu2 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.13ubuntu1 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.4ubuntu3 libdw1_0.190-1 libelf1_0.190-1 libexpat1_2.6.0-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-13ubuntu1 libgcc-s1_14-20240201-3ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: blasr Binary: blasr Architecture: any Version: 5.3.5+dfsg-6build4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Testsuite: autopkgtest 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-4~) Package-List: blasr deb science optional arch=any Checksums-Sha1: 334132438305cfaf3d7ee6208bcb4cc4b493be5d 124460 blasr_5.3.5+dfsg.orig.tar.xz e12761d7cd9ef31aeda4c0505d41121dd8f7e301 11544 blasr_5.3.5+dfsg-6build4.debian.tar.xz Checksums-Sha256: 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9yjG2XEVrGYKwfsx4QZ5Xd+YdG292hTt5Nl1eGmvPRfthpsXX0yMZMT7AB797VDQ UzV4aPbhkNa4VxFN0OPZb9flG54lB0/grXfUD9SXB63ewbFpASeF8XnF36wTyTKp 9FsJc9faFfhnE9Lsp89vvh9lBR152gHiurJ3H4niURgPQBcq/pw= =nHgw -----END PGP SIGNATURE----- gpgv: Signature made Sun Feb 18 21:00:08 2024 UTC gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./blasr_5.3.5+dfsg-6build4.dsc: no acceptable signature found dpkg-source: info: extracting blasr in /<> dpkg-source: info: unpacking blasr_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.5+dfsg-6build4.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-27790033 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27790033 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27790033 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-6build4 dpkg-buildpackage: info: source distribution noble 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 '/<>' LDFLAGS="-L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu -Dpython.bytecompile=-1 -Dtests=false The Meson build system Version: 1.3.2 Source dir: /<> Build dir: /<>/obj-aarch64-linux-gnu Build type: native build Project name: blasr Project version: 5.3.5 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-13ubuntu1) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 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: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.5 Run-time dependency zlib found: YES 1.3 Run-time dependency htslib found: YES 1.19 Library pbcopper found: YES Configuring BlasrVersion.h using configuration 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 python.bytecompile: -1 tests : false Found ninja-1.11.1 at /usr/bin/ninja make[1]: Leaving directory '/<>' 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 5.3.5 /<> @BLASR_GIT_SHA1@ '(.*)' 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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 | ^~~~ [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../extrautils/SWMatcher.cpp:2: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63, from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamToM4.cpp:19: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SDPMatcher.cpp:3: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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/hdf/BufferedHDF2DArray.hpp:12, from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:11, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamToCmpH5.cpp:1: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79: /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); /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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamFilter.cpp:29: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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++ -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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/stl_tree.h:64, from /usr/include/c++/13/map:62, from ../utils/LoadPulses.cpp:6: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [20/25] rm -f libblasr_impl.a && gcc-ar csrDT 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 [21/25] 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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/ToAfg.cpp:6: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [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 -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 [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 -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 [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 -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../iblasr/BlasrHeaders.h:59, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5: ../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: /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: ../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: /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: /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:170:25: 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:30:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 30 | if (dynamic_cast(&read) == NULL) { | ^ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:19:72: note: ‘read’ declared here 19 | void AlignmentToBamRecord(T_AlignmentCandidate &alignment, T_Sequence &read, T_Sequence &subread, | ~~~~~~~~~~~~^~~~ 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: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:538:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; 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: /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); | ^~~~~~~~ /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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../iblasr/BlasrHeaders.h:10: /usr/include/c++/13/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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: /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++/13/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: /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); | ~~~~~~^~~~ /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] /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); | ~~~~~~^~~~ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘AlignmentToBamRecord(AlignmentCandidate&, SMRTSequence&, SMRTSequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool)void’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:30:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 30 | 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 -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/blasr-5.3.5+dfsg-6build4 -DHAVE_HDF5_1_10_1 -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 debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/<>' 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 /<>/debian/blasr/usr/bin Installing sawriter to /<>/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/sawriter: Unknown DWARF DW_FORM_0x1f20 dc491f5f4f94eb570c4a4454d8183f39ea97d61d debugedit: debian/blasr/usr/bin/blasr: Unknown DWARF DW_FORM_0x1f21 aff0985d0c1459a03ed73834e8623ca95ead8bd2 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 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgstriptranslations: processing blasr-dbgsym (in debian/.debhelper/blasr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr pkgstripfiles: Running PNG optimization (using 4 cpus) for package blasr ... pkgstripfiles: processing control file: debian/.debhelper/blasr/dbgsym-root/DEBIAN/control, package blasr-dbgsym, directory debian/.debhelper/blasr/dbgsym-root pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr-dbgsym' in 'debian/.debhelper/scratch-space/build-blasr/blasr-dbgsym_5.3.5+dfsg-6build4_arm64.deb'. dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-6build4_arm64.deb'. Renaming blasr-dbgsym_5.3.5+dfsg-6build4_arm64.deb to blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb dpkg-genbuildinfo --build=any -O../blasr_5.3.5+dfsg-6build4_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../blasr_5.3.5+dfsg-6build4_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 2024-02-18T21:04:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-6build4_arm64.changes: --------------------------------------- Format: 1.8 Date: Sun, 18 Feb 2024 16:00:02 -0500 Source: blasr Binary: blasr Built-For-Profiles: noudeb Architecture: arm64 Version: 5.3.5+dfsg-6build4 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bícha Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.5+dfsg-6build4) noble; urgency=medium . * Rebuild against latest pbcopper Checksums-Sha1: 99e9687568f0fdb23d88697125d224a55ce2d6a0 2770552 blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb b0d2f44a104a1414dac03b1875510776cf36ee3a 8916 blasr_5.3.5+dfsg-6build4_arm64.buildinfo eeb9ab49fec6f35fc82f386f72615dff26e742a7 212452 blasr_5.3.5+dfsg-6build4_arm64.deb Checksums-Sha256: b3878c20f994cc92eee32775535cdac1ada79267f653142236123e3d745eecc0 2770552 blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb 34b887e42d7f2239f825ac9197ffd382a0721d85c726373c9b181f7f7c740404 8916 blasr_5.3.5+dfsg-6build4_arm64.buildinfo 3dd6f6f95699613f016512c6999e4e5a7a439c5961a74814450fbc3065d1bbc5 212452 blasr_5.3.5+dfsg-6build4_arm64.deb Files: af7405e4cd8e7ab222e36ef45aed55db 2770552 debug optional blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb 09669f463226e844d8bb4f99dcd09007 8916 science optional blasr_5.3.5+dfsg-6build4_arm64.buildinfo 38b8c0975c652f4215eefad0f9c99485 212452 science optional blasr_5.3.5+dfsg-6build4_arm64.deb /<>/blasr_5.3.5+dfsg-6build4_arm64.changes.new could not be renamed to /<>/blasr_5.3.5+dfsg-6build4_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: blasr Binary: blasr blasr-dbgsym Architecture: arm64 Version: 5.3.5+dfsg-6build4 Checksums-Md5: af7405e4cd8e7ab222e36ef45aed55db 2770552 blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb 38b8c0975c652f4215eefad0f9c99485 212452 blasr_5.3.5+dfsg-6build4_arm64.deb Checksums-Sha1: 99e9687568f0fdb23d88697125d224a55ce2d6a0 2770552 blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb eeb9ab49fec6f35fc82f386f72615dff26e742a7 212452 blasr_5.3.5+dfsg-6build4_arm64.deb Checksums-Sha256: b3878c20f994cc92eee32775535cdac1ada79267f653142236123e3d745eecc0 2770552 blasr-dbgsym_5.3.5+dfsg-6build4_arm64.ddeb 3dd6f6f95699613f016512c6999e4e5a7a439c5961a74814450fbc3065d1bbc5 212452 blasr_5.3.5+dfsg-6build4_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Sun, 18 Feb 2024 21:04:04 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.42-2ubuntu1), binutils-aarch64-linux-gnu (= 2.42-2ubuntu1), binutils-common (= 2.42-2ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), cmake (= 3.28.3-1), cmake-data (= 3.28.3-1), coreutils (= 9.4-2ubuntu3), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-13ubuntu1), cpp-13-aarch64-linux-gnu (= 13.2.0-13ubuntu1), cpp-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.86), debhelper (= 13.13ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.4ubuntu3), dpkg-dev (= 1.22.4ubuntu3), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-13ubuntu1), g++-13-aarch64-linux-gnu (= 13.2.0-13ubuntu1), g++-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-13ubuntu1), gcc-13-aarch64-linux-gnu (= 13.2.0-13ubuntu1), gcc-13-base (= 13.2.0-13ubuntu1), gcc-14-base (= 14-20240201-3ubuntu1), gcc-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), googletest (= 1.14.0-1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hdf5-helpers (= 1.10.10+repack-3ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-4ubuntu1), libaec-dev (= 1.1.2-1), libaec0 (= 1.1.2-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.7.2-1ubuntu2), libasan8 (= 14-20240201-3ubuntu1), libatomic1 (= 14-20240201-3ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2), libaudit1 (= 1:3.1.2-2), libbinutils (= 2.42-2ubuntu1), libblasr-dev (= 5.3.5+dfsg-6build3), libblasr5.3.5 (= 5.3.5+dfsg-6build3), libblkid1 (= 2.39.2-6ubuntu1), libboost-dev (= 1.83.0.1ubuntu2), libboost1.83-dev (= 1.83.0-2ubuntu1), libbrotli1 (= 1.1.0-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.39-0ubuntu1), libc-dev-bin (= 2.39-0ubuntu1), libc6 (= 2.39-0ubuntu1), libc6-dev (= 2.39-0ubuntu1), libcap-ng0 (= 0.8.4-2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 14-20240201-3ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-2ubuntu1), libctf0 (= 2.42-2ubuntu1), libcurl3-gnutls (= 8.5.0-2ubuntu2), libcurl4 (= 8.5.0-2ubuntu2), libcurl4-gnutls-dev (= 8.5.0-2ubuntu2), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.13ubuntu1), libdeflate-dev (= 1.19-1), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.4ubuntu3), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libexpat1 (= 2.6.0-1), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-13ubuntu1), libgcc-s1 (= 14-20240201-3ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 14-20240201-3ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.3-1ubuntu1), libgomp1 (= 14-20240201-3ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.42-2ubuntu1), libgssapi-krb5-2 (= 1.20.1-5build1), libgtest-dev (= 1.14.0-1), libhdf5-103-1 (= 1.10.10+repack-3ubuntu1), libhdf5-cpp-103-1 (= 1.10.10+repack-3ubuntu1), libhdf5-dev (= 1.10.10+repack-3ubuntu1), libhdf5-fortran-102 (= 1.10.10+repack-3ubuntu1), libhdf5-hl-100 (= 1.10.10+repack-3ubuntu1), libhdf5-hl-cpp-100 (= 1.10.10+repack-3ubuntu1), libhdf5-hl-fortran-100 (= 1.10.10+repack-3ubuntu1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.19+ds-1), libhts3 (= 1.19+ds-1), libhtscodecs2 (= 1.6.0-1), libhwasan0 (= 14-20240201-3ubuntu1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3), libitm1 (= 14-20240201-3ubuntu1), libjansson4 (= 2.14-2), libjpeg-dev (= 8c-2ubuntu11), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg-turbo8-dev (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjpeg8-dev (= 8c-2ubuntu11), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu1), liblsan0 (= 14-20240201-3ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.5-0.3), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.59.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpbbam-dev (= 2.4.0+dfsg-1build1), libpbbam2.4.0 (= 2.4.0+dfsg-1build1), libpbcopper-dev (= 2.3.0+dfsg-2), libpbcopper2.3.0 (= 2.3.0+dfsg-2), libpbdata-dev (= 5.3.5+dfsg-6build3), libpbihdf-dev (= 5.3.5+dfsg-6build3), libpbseq-dev (= 5.3.5+dfsg-6build3), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libproc2-0 (= 2:4.0.4-2ubuntu1), libpsl5 (= 0.21.2-1build1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.12-minimal (= 3.12.2-1), libpython3.12-stdlib (= 3.12.2-1), libreadline8 (= 8.2-3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.5-1ubuntu1), libselinux1 (= 3.5-2build1), libsframe1 (= 2.42-2ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libsqlite3-0 (= 3.45.1-1), libssh-4 (= 0.10.6-2), libssl-dev (= 3.0.10-1ubuntu4), libssl3 (= 3.0.10-1ubuntu4), libstdc++-13-dev (= 13.2.0-13ubuntu1), libstdc++6 (= 14-20240201-3ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.2-3ubuntu2), libsz2 (= 1.1.2-1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libtsan2 (= 14-20240201-3ubuntu1), libubsan1 (= 14-20240201-3ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libuv1 (= 1.46.0-3ubuntu1), libxml2 (= 2.9.14+dfsg-1.3ubuntu1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-11.11), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 46), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), meson (= 1.3.2-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), ninja-build (= 1.11.1-2), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), python3 (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.12.1-0ubuntu1), python3-pkg-resources (= 68.1.2-2), python3-setuptools (= 68.1.2-2), python3.12 (= 3.12.2-1), python3.12-minimal (= 3.12.2-1), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1708290002" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-6build4_arm64.deb ---------------------------------- new Debian package, version 2.0. size 212452 bytes: control archive=1113 bytes. 895 bytes, 15 lines control 913 bytes, 14 lines md5sums Package: blasr Version: 5.3.5+dfsg-6build4 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 612 Depends: libblasr5.3.5 (>= 5.3.5+dfsg), libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libhdf5-cpp-103-1 (>= 1.10.5), libpbbam2.4.0 (>= 2.4.0+dfsg), libpbcopper2.3.0 (>= 2.3.0+dfsg), libstdc++6 (>= 13.1), libpbseq (>= 5.3.5+dfsg-4~) 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. drwxr-xr-x root/root 0 2024-02-18 21:00 ./ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/bin/ -rwxr-xr-x root/root 526800 2024-02-18 21:00 ./usr/bin/blasr -rwxr-xr-x root/root 67840 2024-02-18 21:00 ./usr/bin/sawriter drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/doc/blasr/ -rw-r--r-- root/root 1291 2021-02-18 10:03 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 208 2022-12-05 19:49 ./usr/share/doc/blasr/README.source -rw-r--r-- root/root 542 2022-12-05 19:49 ./usr/share/doc/blasr/README.test -rw-r--r-- root/root 41 2022-12-05 19:49 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 1587 2024-02-18 21:00 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2196 2022-12-05 19:49 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/doc/blasr/examples/ -rw-r--r-- root/root 65 2022-12-05 19:49 ./usr/share/doc/blasr/examples/query.fasta -rw-r--r-- root/root 72 2022-12-05 19:49 ./usr/share/doc/blasr/examples/ref.fa -rw-r--r-- root/root 1067 2022-12-05 19:49 ./usr/share/doc/blasr/run-unit-test drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 163 2022-12-05 19:49 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/man/ drwxr-xr-x root/root 0 2024-02-18 21:00 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2024-02-18 21:00 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2024-02-18 21:00 ./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: 123396 Build-Time: 74 Distribution: noble-proposed Host Architecture: arm64 Install-Time: 23 Job: blasr_5.3.5+dfsg-6build4.dsc Machine Architecture: arm64 Package: blasr Package-Time: 97 Source-Version: 5.3.5+dfsg-6build4 Space: 123396 Status: successful Version: 5.3.5+dfsg-6build4 -------------------------------------------------------------------------------- Finished at 2024-02-18T21:04:04Z Build needed 00:01:37, 123396k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27790033 Scanning for processes to kill in build PACKAGEBUILD-27790033