https://launchpad.net/ubuntu/+source/shasta/0.11.1-5/+build/28433581 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-119 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~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... 9 May 05:25:42 ntpdate[1908]: adjust time server 10.131.248.1 offset 0.001609 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28433581 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-28433581 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28433581 Starting target for build PACKAGEBUILD-28433581 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28433581 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28433581 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28433581 Updating target for build PACKAGEBUILD-28433581 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [73.4 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [64.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [64.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.4 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 Packages [1401 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 Packages [15.3 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [6022 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [183 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [65.6 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [998 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [374 kB] Fetched 25.1 MB in 3s (7227 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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 177 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 79.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.3 [8106 B] Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB] Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.5 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libacl1 amd64 2.3.2-2 [16.8 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapparmor1 amd64 4.0.1-0ubuntu1 [49.9 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcap-ng0 amd64 0.8.5-1 [15.2 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libblkid1 amd64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap2 amd64 1:2.66-5ubuntu2 [30.0 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt-dev amd64 1:4.4.36-4build1 [112 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt1 amd64 1:4.4.36-4build1 [82.3 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error0 amd64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcrypt20 amd64 1.10.3-2build1 [532 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [127 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libzstd1 amd64 1.5.5+dfsg2-2build1 [299 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libkmod2 amd64 31+20240202-2ubuntu7 [51.7 kB] Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblz4-1 amd64 1.9.4-2 [62.9 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu2 [227 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libmount1 amd64 2.39.3-9ubuntu6 [134 kB] Get:29 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl-modules-5.38 all 5.38.2-4 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B] Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libperl5.38t64 amd64 5.38.2-4 [4870 kB] Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl amd64 5.38.2-4 [231 kB] Get:35 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl-base amd64 5.38.2-4 [1823 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu5 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B] Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nis amd64 3.1-0ubuntu7 [26.5 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu8.1 [20.4 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu7 [67.4 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu8.1 [2124 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-0ubuntu8.1 [3265 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-0ubuntu8.1 [682 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd-shared amd64 255.4-1ubuntu8 [2067 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu4 [266 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-sysv amd64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd amd64 255.4-1ubuntu8 [3471 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd0 amd64 255.4-1ubuntu8 [429 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapt-pkg6.0t64 amd64 2.9.2 [987 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu2 [299 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 libunistring5 amd64 1.2-1 [539 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3.1 [998 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt amd64 2.9.2 [1403 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt-utils amd64 2.9.2 [223 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu1 [51.9 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules amd64 1.5.3-7ubuntu1 [284 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB] Get:66 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-14-base amd64 14-20240429-1ubuntu1 [48.0 kB] Get:67 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgcc-s1 amd64 14-20240429-1ubuntu1 [78.3 kB] Get:68 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libstdc++6 amd64 14-20240429-1ubuntu1 [794 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 libudev1 amd64 255.4-1ubuntu8 [174 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libxxhash0 amd64 0.8.2-2build1 [24.1 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu6 [253 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main amd64 libffi8 amd64 3.4.6-1build1 [24.7 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 libidn2-0 amd64 2.3.7-2build1 [66.2 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 libtasn1-6 amd64 4.19.0-3build1 [43.9 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 base-passwd amd64 3.6.3build1 [51.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 libassuan0 amd64 2.5.6-1build1 [37.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsqlite3-0 amd64 3.45.3-1 [701 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg amd64 2.4.4-2ubuntu17 [565 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 readline-common all 8.2-4build1 [56.5 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu2 [148 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu2 [108 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg-agent amd64 2.4.4-2ubuntu17 [227 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgconf amd64 2.4.4-2ubuntu17 [103 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 libnpth0t64 amd64 1.6-3.1build1 [8378 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgv amd64 2.4.4-2ubuntu17 [157 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam0g amd64 1.5.3-7ubuntu1 [67.8 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 libargon2-1 amd64 0~20190702+dfsg-4build1 [20.8 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 libjson-c5 amd64 0.17-1build1 [35.3 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 libuuid1 amd64 2.39.3-9ubuntu6 [35.2 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libfdisk1 amd64 2.39.3-9ubuntu6 [146 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 mount amd64 2.39.3-9ubuntu6 [118 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu4 [22.8 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 linux-libc-dev amd64 6.8.0-31.31 [1598 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.1ubuntu1 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 debianutils amd64 5.17build1 [89.9 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdutils amd64 1:2.39.3-9ubuntu6 [95.0 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main amd64 coreutils amd64 9.4-3ubuntu6 [1412 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main amd64 tar amd64 1.35+dfsg-3build1 [253 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg amd64 1.22.6ubuntu10 [1283 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 diffutils amd64 1:3.10-1build1 [177 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 findutils amd64 4.9.0-5build1 [298 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 grep amd64 3.11-4build1 [162 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 gzip amd64 1.12-1ubuntu3 [98.8 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 hostname amd64 3.23+nmu2ubuntu2 [11.1 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 login amd64 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu2 [188 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 sed amd64 4.9-2build1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main amd64 util-linux amd64 2.39.3-9ubuntu6 [1127 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main amd64 sysvinit-utils amd64 3.08-6ubuntu3 [34.2 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu4 [22.5 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu4 [222 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu4 [601 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu6 [64.8 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main amd64 uuid-runtime amd64 2.39.3-9ubuntu6 [33.1 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main amd64 libattr1 amd64 1:2.5.2-1build1 [11.3 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main amd64 libmd0 amd64 1.1.0-2build1 [27.0 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libsepol2 amd64 3.5-2build1 [303 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu3 [845 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu4 [17.0 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main amd64 mawk amd64 1.3.4.20240123-1build1 [127 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main amd64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 bash-completion all 1:2.13.0-1 [205 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdextrautils amd64 2.39.3-9ubuntu6 [73.8 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main amd64 libip4tc2 amd64 1.8.10-3ubuntu2 [23.3 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 psmisc amd64 23.7-1build1 [179 kB] Get:153 http://ftpmaster.internal/ubuntu 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Get:163 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libubsan1 amd64 14-20240429-1ubuntu1 [1175 kB] Get:164 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 g++-13 amd64 13.2.0-24ubuntu1 [15.0 kB] Get:165 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-24ubuntu1 [2400 kB] Get:166 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgomp1 amd64 14-20240429-1ubuntu1 [148 kB] Get:167 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libitm1 amd64 14-20240429-1ubuntu1 [28.9 kB] Get:168 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libatomic1 amd64 14-20240429-1ubuntu1 [10.4 kB] Get:169 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libasan8 amd64 14-20240429-1ubuntu1 [3025 kB] Get:170 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblsan0 amd64 14-20240429-1ubuntu1 [1313 kB] Get:171 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libhwasan0 amd64 14-20240429-1ubuntu1 [1632 kB] Get:172 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libquadmath0 amd64 14-20240429-1ubuntu1 [153 kB] Get:173 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13 amd64 13.2.0-24ubuntu1 [484 kB] Get:174 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgcc-13-dev amd64 13.2.0-24ubuntu1 [2688 kB] Get:175 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtsan2 amd64 14-20240429-1ubuntu1 [2735 kB] Get:176 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcc1-0 amd64 14-20240429-1ubuntu1 [47.7 kB] Get:177 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cpp-13 amd64 13.2.0-24ubuntu1 [1032 B] Get:178 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13-base amd64 13.2.0-24ubuntu1 [49.3 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpfr6 amd64 4.2.1-1build1 [355 kB] Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] Get:182 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-24ubuntu1 [21.9 MB] Get:183 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-24ubuntu1 [12.5 MB] Get:184 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-24ubuntu1 [11.2 MB] Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:190 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:192 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main amd64 patch amd64 2.7.6-7build3 [104 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main amd64 make amd64 4.3-4.1build2 [180 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/main amd64 lto-disabled-list all 48 [12.3 kB] Get:196 http://ftpmaster.internal/ubuntu oracular/main amd64 libfakeroot amd64 1.34-1 [32.4 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/main amd64 fakeroot amd64 1.34-1 [67.2 kB] Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile-bin amd64 1.17-1build3 [11.2 kB] Get:199 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile1 amd64 1.17-1build3 [6840 B] Get:200 http://ftpmaster.internal/ubuntu oracular/main amd64 lockfile-progs amd64 0.1.19+nmu1 [8854 B] Preconfiguring packages ... 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Setting up liblsan0:amd64 (14-20240429-1ubuntu1) ... Setting up libitm1:amd64 (14-20240429-1ubuntu1) ... Setting up libctf0:amd64 (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-24ubuntu1) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... 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 perl (5.38.2-4) ... Setting up libgprofng0:amd64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19+nmu1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:amd64 (8.2-4build1) ... Setting up libgcc-13-dev:amd64 (13.2.0-24ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:amd64 (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:amd64 (13.2.0-24ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-24ubuntu1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-24ubuntu1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Setting up gcc-13 (13.2.0-24ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build3) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-24ubuntu1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:amd64 (3.1-0ubuntu7) ... Setting up libnsl-dev:amd64 (1.3.0-3build3) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-24ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15996 files and directories currently installed.) Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ... 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-28433581 amd64 oracular-proposed -c chroot:build-PACKAGEBUILD-28433581 --arch=amd64 --dist=oracular-proposed --nolog -A shasta_0.11.1-5.dsc Initiating build PACKAGEBUILD-28433581 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-119.buildd +==============================================================================+ | shasta 0.11.1-5 (amd64) Thu, 09 May 2024 05:26:25 +0000 | +==============================================================================+ Package: shasta Version: 0.11.1-5 Source Version: 0.11.1-5 Distribution: oracular-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28433581/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/shasta-r4fyL9/resolver-3Nj7DE' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- shasta_0.11.1-5.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/shasta-r4fyL9/shasta-0.11.1' with '<>' I: NOTICE: Log filtering will replace 'build/shasta-r4fyL9' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev, libcereal-dev, libblas-dev, liblapack-dev, gfortran, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev, libcereal-dev, libblas-dev, liblapack-dev, gfortran, 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 [501 B] Get:5 copy:/<>/apt_archive ./ Packages [569 B] Fetched 2027 B in 0s (0 B/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 debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 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 chrpath cmake cmake-data debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcereal-dev libcpu-features-dev libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm17t64 liblmdb0 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpng-dev libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libspoa-dev libspoa7.0.0 libssh-4 libsub-override-perl libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-bin mpi-default-dev ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client patchelf po-debconf pybind11-dev python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-dev python3-docutils python3-idna python3-imagesize python3-jinja2 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-urllib3 python3.12 python3.12-dev python3.12-minimal rapidjson-dev sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc graphviz libboost1.83-doc gccxml libboost-contract1.83-dev libmpfrc++-dev libntl-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-stemmer dvipng fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax python3-lib2to3 python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.12-venv python3.12-doc binfmt-support rapidjson-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl libldap-common libcoarrays-openmpi-dev libpng-tools publicsuffix libsasl2-modules xauth libmail-sendmail-perl libeigen3-dev libpaper-utils python3-pil python3-numpy The following NEW packages will be installed: autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcereal-dev libcpu-features-dev libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm17t64 liblmdb0 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpng-dev libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libspoa-dev libspoa7.0.0 libssh-4 libsub-override-perl libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-bin mpi-default-dev ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client patchelf po-debconf pybind11-dev python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-dev python3-docutils python3-idna python3-imagesize python3-jinja2 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-urllib3 python3.12 python3.12-dev python3.12-minimal rapidjson-dev sbuild-build-depends-main-dummy sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 281 newly installed, 0 to remove and 0 not upgraded. Need to get 216 MB of archives. After this operation, 1094 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [788 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12-minimal amd64 3.12.3-1 [833 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libexpat1 amd64 2.6.2-1 [86.9 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 python3.12-minimal amd64 3.12.3-1 [2343 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-minimal amd64 3.12.3-0ubuntu1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [2067 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3.12 amd64 3.12.3-1 [651 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3-stdlib amd64 3.12.3-0ubuntu1 [9890 B] Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 python3 amd64 3.12.3-0ubuntu1 [24.1 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 sgml-base all 1.31 [11.4 kB] Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libbsd0 amd64 0.12.2-1 [41.2 kB] Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libelf1t64 amd64 0.191-1 [57.5 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu74 amd64 74.2-1ubuntu3 [10.9 MB] Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pygments all 2.17.2+dfsg-1 [819 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB] Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 file amd64 1:5.45-3build1 [22.0 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext-base amd64 0.21-14ubuntu2 [38.4 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libuchardet0 amd64 0.0.8-1build1 [75.3 kB] Get:24 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 groff-base amd64 1.23.0-4 [1020 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libnl-3-200 amd64 3.7.0-0.3build1 [55.6 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libnl-route-3-200 amd64 3.7.0-0.3build1 [189 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libibverbs1 amd64 50.0-2build2 [67.8 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 ibverbs-providers amd64 50.0-2build2 [374 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 libcbor0.10 amd64 0.10.2-1.2ubuntu2 [25.8 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-common all 2.4.120-2build1 [8096 B] Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm2 amd64 2.4.120-2build1 [40.5 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libedit2 amd64 3.1-20230828-1build1 [97.6 kB] Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libfido2-1 amd64 1.14.0-1build3 [83.5 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 liblmdb0 amd64 0.9.31-1build1 [48.1 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.61.0-1 [74.8 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 libnuma1 amd64 2.0.18-1build1 [23.3 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libpipeline1 amd64 1.5.7-2 [23.6 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libpsl5t64 amd64 0.21.2-1.1build1 [57.1 kB] Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libuv1t64 amd64 1.48.0-1.1build1 [97.3 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libxau6 amd64 1:1.0.9-1build6 [7160 B] Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu6 [10.3 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb1 amd64 1.15-1ubuntu2 [47.7 kB] Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libx11-data all 2:1.8.7-1build1 [115 kB] Get:44 http://ftpmaster.internal/ubuntu oracular/main amd64 libx11-6 amd64 2:1.8.7-1build1 [650 kB] Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 libxext6 amd64 2:1.3.4-1build2 [30.4 kB] Get:46 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 man-db amd64 2.12.1-1 [1236 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-client amd64 1:9.6p1-3ubuntu13 [905 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 m4 amd64 1.4.19-4build1 [244 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 autoconf all 2.71-3 [339 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main amd64 autopoint all 0.21-14ubuntu2 [422 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 chrpath amd64 0.16-2build1 [12.8 kB] Get:54 http://ftpmaster.internal/ubuntu oracular/main amd64 libarchive13t64 amd64 3.7.2-2 [381 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libbrotli1 amd64 1.1.0-2build2 [331 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-5ubuntu3 [20.3 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-5ubuntu3 [53.2 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu8 [195 kB] Get:59 http://ftpmaster.internal/ubuntu oracular/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build7 [56.3 kB] Get:60 http://ftpmaster.internal/ubuntu oracular/main amd64 libssh-4 amd64 0.10.6-2build2 [188 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcurl4t64 amd64 8.5.0-2ubuntu10.1 [341 kB] Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 libjsoncpp25 amd64 1.9.5-6build1 [82.8 kB] Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 librhash0 amd64 1.4.3-3build1 [129 kB] Get:64 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cmake-data all 3.29.2-2 [2193 kB] Get:65 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cmake amd64 3.29.2-2 [11.4 MB] Get:66 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main amd64 libtool all 2.4.7-7build1 [166 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-autoreconf all 20 [16.1 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:73 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdw1t64 amd64 0.191-1 [265 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 debugedit amd64 1:5.0-5build2 [46.1 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 dwz amd64 0.15-1build6 [115 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext amd64 0.21-14ubuntu2 [864 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:79 http://ftpmaster.internal/ubuntu oracular/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:81 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 dh-python all 6.20240422 [110 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 xml-core all 0.19 [20.3 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 docutils-common all 0.20.1+dfsg-3 [132 kB] Get:84 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgfortran5 amd64 14-20240429-1ubuntu1 [928 kB] Get:85 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgfortran-13-dev amd64 13.2.0-24ubuntu1 [942 kB] Get:86 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24ubuntu1 [11.6 MB] Get:87 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gfortran-13 amd64 13.2.0-24ubuntu1 [11.9 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 icu-devtools amd64 74.2-1ubuntu3 [212 kB] Get:91 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libllvm17t64 amd64 1:17.0.6-12 [26.2 MB] Get:92 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-amdgpu1 amd64 2.4.120-2build1 [20.2 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] Get:95 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamdhip64-5 amd64 5.7.1-3 [9621 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas-dev amd64 3.12.0-3build1 [170 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost1.83-dev amd64 1.83.0-2.1ubuntu3 [10.7 MB] Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-dev amd64 1.83.0.1ubuntu2 [4308 B] Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost1.83-tools-dev amd64 1.83.0-2.1ubuntu3 [1402 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-tools-dev amd64 1.83.0.1ubuntu2 [4238 B] Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-atomic1.83.0 amd64 1.83.0-2.1ubuntu3 [240 kB] Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-atomic1.83-dev amd64 1.83.0-2.1ubuntu3 [235 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-atomic-dev amd64 1.83.0.1ubuntu2 [4360 B] Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-2.1ubuntu3 [245 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-chrono1.83-dev amd64 1.83.0-2.1ubuntu3 [246 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-chrono-dev amd64 1.83.0.1ubuntu2 [4672 B] Get:109 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-container1.83.0 amd64 1.83.0-2.1ubuntu3 [261 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-container1.83-dev amd64 1.83.0-2.1ubuntu3 [267 kB] Get:111 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-container-dev amd64 1.83.0.1ubuntu2 [4530 B] Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-date-time1.83.0 amd64 1.83.0-2.1ubuntu3 [236 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-serialization1.83.0 amd64 1.83.0-2.1ubuntu3 [341 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-serialization1.83-dev amd64 1.83.0-2.1ubuntu3 [387 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-date-time1.83-dev amd64 1.83.0-2.1ubuntu3 [239 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-system1.83.0 amd64 1.83.0-2.1ubuntu3 [236 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-system1.83-dev amd64 1.83.0-2.1ubuntu3 [231 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-thread1.83.0 amd64 1.83.0-2.1ubuntu3 [276 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-thread1.83-dev amd64 1.83.0-2.1ubuntu3 [282 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-context1.83.0 amd64 1.83.0-2.1ubuntu3 [237 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-context1.83-dev amd64 1.83.0-2.1ubuntu3 [232 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-context-dev amd64 1.83.0.1ubuntu2 [4276 B] Get:123 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-coroutine1.83.0 amd64 1.83.0-2.1ubuntu3 [234 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-coroutine1.83-dev amd64 1.83.0-2.1ubuntu3 [237 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-coroutine-dev amd64 1.83.0.1ubuntu2 [4344 B] Get:126 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-date-time-dev amd64 1.83.0.1ubuntu2 [4058 B] Get:127 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-exception1.83-dev amd64 1.83.0-2.1ubuntu3 [229 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-exception-dev amd64 1.83.0.1ubuntu2 [4058 B] Get:129 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-2.1ubuntu3 [283 kB] Get:130 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-filesystem1.83-dev amd64 1.83.0-2.1ubuntu3 [301 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-fiber1.83.0 amd64 1.83.0-2.1ubuntu3 [254 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-fiber1.83-dev amd64 1.83.0-2.1ubuntu3 [268 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-fiber-dev amd64 1.83.0.1ubuntu2 [4486 B] Get:134 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-filesystem-dev amd64 1.83.0.1ubuntu2 [4096 B] Get:135 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-graph1.83.0 amd64 1.83.0-2.1ubuntu3 [360 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-regex1.83.0 amd64 1.83.0-2.1ubuntu3 [339 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu-dev amd64 74.2-1ubuntu3 [11.9 MB] Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-regex1.83-dev amd64 1.83.0-2.1ubuntu3 [355 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-test1.83.0 amd64 1.83.0-2.1ubuntu3 [454 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-test1.83-dev amd64 1.83.0-2.1ubuntu3 [566 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-graph1.83-dev amd64 1.83.0-2.1ubuntu3 [399 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-graph-dev amd64 1.83.0.1ubuntu2 [4160 B] Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-9ubuntu2 [91.3 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-9ubuntu2 [7982 B] Get:145 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] Get:146 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm2-2 amd64 11.2.185-2build1 [194 kB] Get:147 http://ftpmaster.internal/ubuntu oracular/main amd64 librdmacm1t64 amd64 50.0-2build2 [70.7 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfabric1 amd64 1.17.0-3build2 [657 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc15 amd64 2.10.0-1build1 [172 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc-plugins amd64 2.10.0-1build1 [15.7 kB] Get:155 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libpmix2t64 amd64 5.0.2-3 [706 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/universe amd64 libucx0 amd64 1.16.0+ds-5ubuntu1 [1140 kB] Get:157 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http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-json1.83.0 amd64 1.83.0-2.1ubuntu3 [365 kB] Get:166 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-json1.83-dev amd64 1.83.0-2.1ubuntu3 [380 kB] Get:167 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-json-dev amd64 1.83.0.1ubuntu2 [4172 B] Get:168 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-locale1.83.0 amd64 1.83.0-2.1ubuntu3 [413 kB] Get:169 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-locale1.83-dev amd64 1.83.0-2.1ubuntu3 [582 kB] Get:170 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-locale-dev amd64 1.83.0.1ubuntu2 [4378 B] Get:171 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-log1.83.0 amd64 1.83.0-2.1ubuntu3 [679 kB] Get:172 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-log1.83-dev amd64 1.83.0-2.1ubuntu3 [937 kB] Get:173 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-log-dev amd64 1.83.0.1ubuntu2 [4260 B] Get:174 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-math1.83.0 amd64 1.83.0-2.1ubuntu3 [440 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-math1.83-dev amd64 1.83.0-2.1ubuntu3 [586 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-math-dev amd64 1.83.0.1ubuntu2 [4264 B] Get:177 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-common all 4.1.6-7ubuntu2 [170 kB] Get:178 http://ftpmaster.internal/ubuntu oracular/main amd64 libnl-3-dev amd64 3.7.0-0.3build1 [99.5 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libnl-route-3-dev amd64 3.7.0-0.3build1 [216 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libibverbs-dev amd64 50.0-2build2 [678 kB] Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 libnuma-dev amd64 2.0.18-1build1 [37.0 kB] Get:182 http://ftpmaster.internal/ubuntu oracular/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] Get:183 http://ftpmaster.internal/ubuntu oracular/main amd64 libltdl-dev amd64 2.4.7-7build1 [168 kB] Get:184 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc-dev amd64 2.10.0-1build1 [268 kB] Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-9ubuntu2 [145 kB] Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-9ubuntu2 [64.2 kB] Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-9ubuntu2 [15.7 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-dev amd64 2.1.12-stable-9ubuntu2 [274 kB] Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Get:190 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libpmix-dev amd64 5.0.2-3 [4042 kB] Get:191 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:192 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-bin amd64 4.1.6-7ubuntu2 [114 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/universe amd64 libopenmpi-dev amd64 4.1.6-7ubuntu2 [864 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/universe amd64 mpi-default-dev amd64 1.15build1 [3154 B] Get:196 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-mpi1.83-dev amd64 1.83.0-2.1ubuntu3 [296 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-mpi-dev amd64 1.83.0.1ubuntu2 [4144 B] Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-python1.83.0 amd64 1.83.0-2.1ubuntu3 [312 kB] Get:199 http://ftpmaster.internal/ubuntu oracular/universe amd64 mpi-default-bin amd64 1.15build1 [2376 B] Get:200 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-mpi-python1.83.0 amd64 1.83.0-2.1ubuntu3 [362 kB] Get:201 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-mpi-python1.83-dev amd64 1.83.0-2.1ubuntu3 [237 kB] Get:202 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-mpi-python-dev amd64 1.83.0.1ubuntu2 [4196 B] Get:203 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-2.1ubuntu3 [242 kB] Get:204 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-numpy1.83-dev amd64 1.83.0-2.1ubuntu3 [247 kB] Get:205 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-numpy-dev amd64 1.83.0.1ubuntu2 [4100 B] Get:206 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1ubuntu3 [320 kB] Get:207 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-program-options1.83-dev amd64 1.83.0-2.1ubuntu3 [388 kB] Get:208 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-program-options-dev amd64 1.83.0.1ubuntu2 [4086 B] Get:209 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12t64 amd64 3.12.3-1 [2339 kB] Get:210 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libexpat1-dev amd64 2.6.2-1 [998 kB] Get:211 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12-dev amd64 3.12.3-1 [5671 kB] Get:212 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3-dev amd64 3.12.3-0ubuntu1 [10.2 kB] Get:213 http://ftpmaster.internal/ubuntu oracular/main amd64 python3.12-dev amd64 3.12.3-1 [498 kB] Get:214 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:215 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-sphinxdoc all 7.2.6-6 [149 kB] Get:216 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dev amd64 3.12.3-0ubuntu1 [26.7 kB] Get:217 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-python1.83-dev amd64 1.83.0-2.1ubuntu3 [337 kB] Get:218 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-python-dev amd64 1.83.0.1ubuntu2 [4344 B] Get:219 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-random1.83.0 amd64 1.83.0-2.1ubuntu3 [242 kB] Get:220 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-random1.83-dev amd64 1.83.0-2.1ubuntu3 [241 kB] Get:221 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-random-dev amd64 1.83.0.1ubuntu2 [4062 B] Get:222 http://ftpmaster.internal/ubuntu oracular/main amd64 libboost-regex-dev amd64 1.83.0.1ubuntu2 [4324 B] Get:223 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-serialization-dev amd64 1.83.0.1ubuntu2 [4280 B] Get:224 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-stacktrace1.83.0 amd64 1.83.0-2.1ubuntu3 [291 kB] Get:225 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-stacktrace1.83-dev amd64 1.83.0-2.1ubuntu3 [247 kB] Get:226 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libboost-type-erasure1.83-dev amd64 1.83.0-2.1ubuntu3 [250 kB] Get:235 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-type-erasure-dev amd64 1.83.0.1ubuntu2 [4162 B] Get:236 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-url1.83.0 amd64 1.83.0-2.1ubuntu3 [343 kB] Get:237 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-url1.83-dev amd64 1.83.0-2.1ubuntu3 [443 kB] Get:238 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-url-dev amd64 1.83.0.1ubuntu2 [4192 B] Get:239 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-wave1.83.0 amd64 1.83.0-2.1ubuntu3 [454 kB] Get:240 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-wave1.83-dev amd64 1.83.0-2.1ubuntu3 [499 kB] Get:241 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-wave-dev amd64 1.83.0.1ubuntu2 [4096 B] Get:242 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-nowide1.83.0 amd64 1.83.0-2.1ubuntu3 [240 kB] Get:243 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-nowide1.83-dev amd64 1.83.0-2.1ubuntu3 [236 kB] Get:244 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-nowide-dev amd64 1.83.0.1ubuntu2 [4136 B] Get:245 http://ftpmaster.internal/ubuntu oracular/universe amd64 libboost-all-dev amd64 1.83.0.1ubuntu2 [2286 B] Get:246 http://ftpmaster.internal/ubuntu oracular/universe amd64 rapidjson-dev all 1.1.0+dfsg2-7.2 [96.7 kB] Get:247 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcereal-dev amd64 1.3.2+dfsg-5 [222 kB] Get:248 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcpu-features-dev amd64 0.9.0-1 [23.8 kB] Get:249 http://ftpmaster.internal/ubuntu oracular/main amd64 libjson-perl all 4.10000-1 [81.9 kB] Get:250 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] Get:251 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack-dev amd64 3.12.0-3build1 [5196 kB] Get:252 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http://ftpmaster.internal/ubuntu oracular/universe amd64 patchelf amd64 0.18.0-1.1build1 [106 kB] Get:262 http://ftpmaster.internal/ubuntu oracular/universe amd64 pybind11-dev all 2.11.1-2 [159 kB] Get:263 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python-babel-localedata all 2.14.0-1 [6385 kB] Get:264 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python3-babel all 2.14.0-1 [96.4 kB] Get:265 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-certifi all 2023.11.17-1 [165 kB] Get:266 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:267 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-roman all 3.3-3 [9632 B] Get:268 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:269 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-idna all 3.6-2 [46.0 kB] Get:270 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-imagesize all 1.4.1-1 [6844 B] Get:271 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-markupsafe amd64 2.1.5-1build2 [12.7 kB] Get:272 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python3-jinja2 all 3.1.3-1 [107 kB] Get:273 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] Get:274 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pybind11 all 2.11.1-2 [167 kB] Get:275 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-urllib3 all 2.0.7-1 [113 kB] Get:276 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:277 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] Get:278 http://ftpmaster.internal/ubuntu oracular/main amd64 sphinx-common all 7.2.6-6 [739 kB] Get:279 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-alabaster all 0.7.12-1 [17.8 kB] Get:280 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-sphinx all 7.2.6-6 [557 kB] Get:281 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-exec amd64 0.29build1 [25.7 kB] Preconfiguring packages ... Fetched 216 MB in 3s (67.4 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 15996 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.3-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.3-1_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16314 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_amd64.deb ... 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Setting up ibverbs-providers:amd64 (50.0-2build2) ... Setting up libspoa-dev:amd64 (4.1.4-1) ... Setting up openssh-client (1:9.6p1-3ubuntu13) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-type-erasure1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up libxext6:amd64 (2:1.3.4-1build2) ... Setting up libboost-random-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-locale-dev:amd64 (1.83.0.1ubuntu2) ... Setting up python3 (3.12.3-0ubuntu1) ... Setting up libpython3.12-dev:amd64 (3.12.3-1) ... Setting up libboost-wave-dev:amd64 (1.83.0.1ubuntu2) ... Setting up man-db (2.12.1-1) ... 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 python3-markupsafe (2.1.5-1build2) ... Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gfortran (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up libboost-container-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-type-erasure-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-context1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... Setting up ncbi-blast+ (2.12.0+ds-4build2) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3build1) ... Setting up libboost-coroutine1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up libboost-fiber1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up python3-snowballstemmer (2.2.0-4build1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libevent-dev (2.1.12-stable-9ubuntu2) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.3-1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up cmake (3.29.2-2) ... Setting up librdmacm1t64:amd64 (50.0-2build2) ... Setting up libboost-coroutine-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-log1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-json-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-regex-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-log-dev (1.83.0.1ubuntu2) ... Setting up libhsakmt1:amd64 (5.7.0-1build1) ... Setting up libboost-thread-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-fiber-dev:amd64 (1.83.0.1ubuntu2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libfabric1:amd64 (1.17.0-3build2) ... Setting up libpython3-dev:amd64 (3.12.3-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up python3-alabaster (0.7.12-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up dh-exec (0.29build1) ... Setting up libboost-context-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libibverbs-dev:amd64 (50.0-2build2) ... Setting up libhwloc-plugins:amd64 (2.10.0-1build1) ... Setting up libboost-graph1.83-dev:amd64 (1.83.0-2.1ubuntu3) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.12.3-0ubuntu1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up libboost-python1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up libhsa-runtime64-1 (5.7.1-2build1) ... Setting up libpmix-dev:amd64 (5.0.2-3) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20240422) ... Setting up libboost-graph-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libboost-python-dev (1.83.0.1ubuntu2) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up libucx0:amd64 (1.16.0+ds-5ubuntu1) ... Setting up libopenmpi3t64:amd64 (4.1.6-7ubuntu2) ... Setting up libboost-mpi1.83.0 (1.83.0-2.1ubuntu3) ... Setting up openmpi-bin (4.1.6-7ubuntu2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libboost-graph-parallel1.83.0 (1.83.0-2.1ubuntu3) ... Setting up mpi-default-bin (1.15build1) ... Setting up libopenmpi-dev:amd64 (4.1.6-7ubuntu2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-python1.83.0 (1.83.0-2.1ubuntu3) ... Setting up libboost-graph-parallel-dev (1.83.0.1ubuntu2) ... Setting up mpi-default-dev (1.15build1) ... Setting up libboost-mpi1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-dev (1.83.0.1ubuntu2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-python-dev (1.83.0.1ubuntu2) ... Setting up libboost-all-dev (1.83.0.1ubuntu2) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for systemd (255.4-1ubuntu8) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64 all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-24ubuntu1 gcc-13_13.2.0-24ubuntu1 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-24ubuntu1 libstdc++6_14-20240429-1ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.13.0-1 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-x86-64-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 chrpath_0.16-2build1 cmake_3.29.2-2 cmake-data_3.29.2-2 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-24ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-24ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-exec_0.29build1 dh-python_6.20240422 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 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openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu3 patch_2.7.6-7build3 patchelf_0.18.0-1.1build1 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-4 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 pybind11-dev_2.11.1-2 python-babel-localedata_2.14.0-1 python3_3.12.3-0ubuntu1 python3-alabaster_0.7.12-1 python3-babel_2.14.0-1 python3-certifi_2023.11.17-1 python3-chardet_5.2.0+dfsg-1 python3-dev_3.12.3-0ubuntu1 python3-docutils_0.20.1+dfsg-3 python3-idna_3.6-2 python3-imagesize_1.4.1-1 python3-jinja2_3.1.3-1 python3-markupsafe_2.1.5-1build2 python3-minimal_3.12.3-0ubuntu1 python3-packaging_24.0-1 python3-pkg-resources_68.1.2-2ubuntu1 python3-pybind11_2.11.1-2 python3-pygments_2.17.2+dfsg-1 python3-requests_2.31.0+dfsg-1ubuntu1 python3-roman_3.3-3 python3-setuptools_68.1.2-2ubuntu1 python3-snowballstemmer_2.2.0-4build1 python3-sphinx_7.2.6-6 python3-urllib3_2.0.7-1 python3.12_3.12.3-1 python3.12-dev_3.12.3-1 python3.12-minimal_3.12.3-1 rapidjson-dev_1.1.0+dfsg2-7.2 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 sgml-base_1.31 sphinx-common_7.2.6-6 systemd_255.4-1ubuntu8 systemd-dev_255.4-1ubuntu8 systemd-sysv_255.4-1ubuntu8 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xml-core_0.19 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shasta Binary: shasta, python3-shasta, python3-shasta-doc Architecture: any-amd64 arm64 all Version: 0.11.1-5 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust , Étienne Mollier Homepage: https://github.com/chanzuckerberg/shasta Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/shasta Vcs-Git: https://salsa.debian.org/med-team/shasta.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev [any-amd64], libcereal-dev, libblas-dev, liblapack-dev, gfortran Package-List: python3-shasta deb python optional arch=any-amd64,arm64 python3-shasta-doc deb doc optional arch=all shasta deb science optional arch=any-amd64,arm64 Checksums-Sha1: 372f39c1423a43164db29c55859397393a436744 3999058 shasta_0.11.1.orig.tar.gz 3b8f0af4fb42b8422b9bcf8bd7ec9dea7840e7f9 10812 shasta_0.11.1-5.debian.tar.xz Checksums-Sha256: 7fdf7cfd939f33a619773f5c6ca56e168b3e1cc77b9b7811a98ec06f6dd8ba9a 3999058 shasta_0.11.1.orig.tar.gz 30ea5aaece2b85383a63f70cbc466691539dae4f97596f0347da567438b526d9 10812 shasta_0.11.1-5.debian.tar.xz Files: c1ec064ed6fe3d2815d70bc3baa2e61f 3999058 shasta_0.11.1.orig.tar.gz b39edce37da1e839159a6cf81bcb9335 10812 shasta_0.11.1-5.debian.tar.xz Dgit: f493a18b33a81eef8875bda2295b0963e5c3164c debian archive/debian/0.11.1-5 https://git.dgit.debian.org/shasta -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmY723MUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp7WhAAuY9zKesQNGrpDu1+wjJBazYUilrC h/3es0PPFNHF9Q8RkwO5Hpx1/RyLkoB06TzMwtu5X7u2NBAe6DQuBYaeYIlDKAzR h6HWXl6Gnnx1zDLlsoVHlreuaWrxbtg5dwTV36dLy2snmwIoUUO49LgOs3H9makD 3BZjef+01BPCwW8VEIRCZAtA2l7QcGw+ntAYieZWlsVQ4/T3K1e+rDmIcrzFudW+ YQG5nZne/M6+CAjy4OT1/o/gjfq8rASGue0DsiOM0YN4SOlVEuK8yyfFI9EU2obS zt9x3aQTObriCgQXoPdTdCUAA775faK4D5numozx+sLY6lsz81tOAU5jEnproqSf 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---------------- 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-28433581 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28433581 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28433581 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 shasta dpkg-buildpackage: info: source version 0.11.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DBUILD_ID=0.11.1 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_ID=0.11.1 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.11.1 -- Configuring done (0.4s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/staticLibrary /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/staticLibrary /<>/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/dynamicLibrary /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/dynamicLibrary /<>/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o [ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /<>/src/Alignment.cpp cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /<>/src/Align4.cpp cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /<>/src/Align4.cpp [ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /<>/src/Alignment.cpp [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /<>/src/AlignmentGraph.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /<>/src/AlignmentGraph.cpp In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/string:42, from /<>/src/string.hpp:4, from /<>/src/PngImage.hpp:6, from /<>/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /<>/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /<>/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /<>/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /<>/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /<>/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /<>/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/string:42, from /<>/src/string.hpp:4, from /<>/src/PngImage.hpp:6, from /<>/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /<>/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /<>/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /<>/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /<>/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /<>/src/AlignmentGraph.cpp:239:34: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /<>/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /<>/src/AssembledSegment.cpp [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /<>/src/AssembledSegment.cpp [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /<>/src/Assembler.cpp [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /<>/src/Assembler.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /<>/src/AssemblerAlign.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /<>/src/AssemblerAlign.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /<>/src/AssemblerAlign1.cpp [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /<>/src/AssemblerAlign1.cpp /<>/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /<>/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ /<>/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /<>/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /<>/src/AssemblerAlign3.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /<>/src/AssemblerAlign3.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /<>/src/AssemblerAlign4.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /<>/src/AssemblerAlign4.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 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-fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /<>/src/AssemblerAlignmentCandidates.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /<>/src/AssemblerAlignmentGraph.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API 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/<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /<>/src/AssemblerAlignments.cpp cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /<>/src/AssemblerAlignments.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /<>/src/AssemblerAnalyzePaths.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /<>/src/AssemblerAnalyzePaths.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /<>/src/AssemblerAssemblyGraph.cpp [ 14%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /<>/src/AssemblerAssemblyGraph.cpp [ 14%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /<>/src/AssemblerAssemblyGraph2.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /<>/src/AssemblerAssemblyGraph2.cpp In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/src/iostream.hpp:4, from /<>/src/ReadId.hpp:11, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /<>/src/AssemblerAssemblyGraph.cpp:1623:53: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /<>/src/LocalAssemblyGraph.hpp:18, from /<>/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /<>/src/AssemblerAssemblyGraph.cpp:1668:57: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In file included from /usr/include/c++/13/bits/char_traits.h:57, from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/src/iostream.hpp:4, from /<>/src/ReadId.hpp:11, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /<>/src/AssemblerAssemblyGraph.cpp:1623:53: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /<>/src/LocalAssemblyGraph.hpp:18, from /<>/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:2005:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /<>/src/AssemblerAssemblyGraph.cpp:1668:57: /usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 15%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerCompressedAssemblyGraph.cpp [ 15%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerCompressedAssemblyGraph.cpp [ 15%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /<>/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 16%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /<>/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /<>/src/AssemblerDetangle.cpp [ 17%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /<>/src/AssemblerDetangle.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /<>/src/AssemblerHttpServer-Alignments.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd 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object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /<>/src/AssemblerHttpServer-AssemblyGraph.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /<>/src/CompactUndirectedGraph.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -c /<>/src/ConfigurationTable.cpp [ 45%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -c /<>/src/ConsensusCaller.cpp [ 45%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -c /<>/src/InducedAlignment.cpp [ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /<>/src/LocalAlignmentCandidateGraph.cpp [ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /<>/src/LocalAlignmentGraph.cpp [ 50%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -c /<>/src/InducedAlignment.cpp [ 51%] 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /<>/src/LocalMarkerGraph-Write.cpp [ 52%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /<>/src/LocalMarkerGraph.cpp [ 52%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o 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/<>/src/LocalReadGraph.cpp [ 53%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -c /<>/src/LongBaseSequence.cpp [ 53%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -c /<>/src/LowHash0.cpp [ 54%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && 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-Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /<>/src/LocalMarkerGraph-Write.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o -c /<>/src/buildId.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o -MF 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CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o -c /<>/src/computeRunLengthRepresentation.cpp [ 67%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -c /<>/src/diploidBayesianPhase.cpp [ 68%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o.d -o 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o -c /<>/src/filesystem.cpp [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o -c /<>/src/html.cpp [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o -c /<>/src/mode3-AssemblyPath.cpp [ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o -c /<>/src/mode3-Detangler.cpp [ 71%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -c /<>/src/mode3-JaccardGraph.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /<>/src/LocalMarkerGraph.cpp [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /<>/src/LocalReadGraph.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /<>/src/mode3-JaccardGraph.hpp:29, from /<>/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -c /<>/src/LongBaseSequence.cpp [ 72%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /<>/src/mode3-LocalAssemblyGraph.cpp [ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /<>/src/mode3-PathGraph.cpp [ 73%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -c /<>/src/LowHash0.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o -c /<>/src/LowHash1.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -c /<>/src/MarkerFinder.cpp [ 75%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -c /<>/src/MarkerGraph.cpp [ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -c /<>/src/mode3.cpp [ 75%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -c /<>/src/MedianConsensusCaller.cpp [ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -c /<>/src/MemoryMappedAllocator.cpp [ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /<>/src/MemoryMappedVector.cpp [ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -c /<>/src/MultithreadedObject.cpp [ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API 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-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -c /<>/src/performanceLog.cpp [ 79%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o cd /<>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. 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CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o /usr/bin/ranlib shasta.a make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 94%] Built target shastaStaticLibrary [ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /<>/src/mode3-LocalAssemblyGraph.cpp [ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /<>/src/mode3-PathGraph.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /<>/src/mode3-JaccardGraph.hpp:29, from /<>/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [ 96%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -c /<>/src/mode3.cpp [ 96%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -c /<>/src/performanceLog.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -c /<>/src/platformDependent.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /<>/src/runCommandWithTimeout.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -c /<>/src/shastaLapack.cpp [ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -c /<>/src/testSpoa.cpp [ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /<>/src/testSubsetGraph.cpp [ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -c /<>/src/timestamp.cpp [100%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ 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CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/dynamicExecutable /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/dynamicExecutable /<>/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /<>/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicExecutable/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /<>/srcMain/main.cpp [100%] Linking CXX executable shastaDynamic cd /<>/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/<>/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.12 -ldl -lm make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v7.2.6 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.a -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.so -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/shastaDynamic -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads1.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads4.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AlignPseudoPaths.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeAlignmentMatrix.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeAssemblyGraphBubbles.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeMode3Subgraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeReadGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Assemble.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AssembleMarkerGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AssembleMarkerGraphVertices.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/AssembleSegment.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CheckConfigurations.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CheckMarkerGraphIsStrandSymmetric.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CleanupDuplicateMarkers.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CleanupRunDirectory.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ClusterMarkerGraphEdgeOrientedReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ColorGfaBySimilarityToSegment.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ColorGfaKeySegments.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ColorGfaWithTwoReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeAlignments.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeAssemblyStatistics.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeMarkerGraphCoverageHistogram.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeMarkerGraphVerticesCoverageData.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeReadGraphConnectedComponents.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ComputeSortedMarkers.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Copy.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CopyDirectory.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateAndCleanupMarkerGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateAssembly.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateAssemblyGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateAssemblyGraphVertices.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateCompressedAssemblyGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateConfigurationTable.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateLocalSubgraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMarkerGraphAndTransitiveReduction.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMarkerGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMarkerGraphEdgesStrict.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMarkerGraphSecondaryEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMarkerGraphVertices.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMode3Detangler.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateMode3PathGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateModules.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateReadGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateReadGraph2.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateReadGraphMode1.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/CreateReadGraphUsingPseudoPaths.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Detangle.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Detangle2.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FastqGzToFasta.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FastqToFasta.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FastqToFastaAll.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindAlignmentCandidatesLowHash0.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindAlignmentCandidatesLowHash1.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindAssemblyGraphBubbles.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindMarkerGraphReverseComplementEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindMarkerGraphReverseComplementVertices.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FindMarkers.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FlagChimericReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FlagCrossStrandReadGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FlagInconsistentAlignments.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/FlagPalindromicReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/GenerateConfig.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/GenerateFeedback.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/GetConfig.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/GetReadId.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/HistogramReadLength.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/InstallPrerequisites-Ubuntu.sh -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Mode2Assembly-A.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Mode2Assembly-B-Prepare.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Mode2Assembly-B.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Mode3Assembly.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/PruneMarkerGraphStrongSubgraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/RandomlySelectKmers.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ReadGraphClustering.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/RemoveReadGraphBridges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/RestoreRun.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/ReverseTransitiveReduction.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/RunAssemblies.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SaveRun.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SelectKmers2.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SelectKmers4.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SelectKmersBasedOnFrequency.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SetMarkerGraphEdgeFlags.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SetupRunDirectory.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SetupSmallRunDirectory.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SimpleBayesianConsensusCallerCreateBuiltin.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SimplifyMarkerGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SplitMarkerGraphSecondaryEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/StepSequence1.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/SummarizeAssemblies.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/Test.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/TestSimpleBayesianConsensusCaller.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/TransitiveReduction.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/TravisCheckBuildMacOS.sh -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/TravisCheckBuildUbuntu.sh -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/VertexCoverageStatisticsByKmerId.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteAlignmentCandidates.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteAlignmentDetails.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteAssemblyGraph.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteBadMarkerGraphVertices.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteFasta.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteGfa.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteGfaBothStrands.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteLocalAlignmentCandidateReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteLocalReadGraphReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteMarkers.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteMarkersFrequency.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteOrientedRead.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteOrientedReadPath.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteOrientedReadsBySegment.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteParallelMarkerGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WritePseudoPath.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteRead.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteReadGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/WriteReads.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/comparePhaseAssignments.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/dset64Test.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/bin/generateBandageLabelsFromAlignment.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-3.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CCS-Dec2019.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-May2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-7.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Sep2020.conf -- Installing: 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/<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-Aug2021.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Phased-May2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-2.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Jan2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Human-SingleFlowcell-May2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/HiFi-Oct2021.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-R10-Slow-Nov2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-OldGuppy-Sep2020.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Dec2019.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Human-SingleFlowcell-Phased-May2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-6.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-R10-Slow-Nov2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Sep2020.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Jun2020.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Phased-Jan2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Jun2020.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Dec2019.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/README.md -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-9.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-R10-Fast-Nov2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-11.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Phased-Oct2021.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-iterative-Sep2020.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-May2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-Jan2022.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-8.csv -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CLR-Dec2019.conf -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/ComputationalMethods.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/index.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/CZI-new-logo.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Performance.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignment.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Markers.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/style.css -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot -- 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/<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Python.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerAlignment.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-Before.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Introduction.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Compatibility.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-5.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/QuickStart.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PhasedRegionsNaming.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Acknowledgments.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Superbubble.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Prerequisites.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MakeRelease.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/ReadGraph1.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/Makefile -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/conf.py -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/index.rst -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/shasta.so -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/README -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/7.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/4.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/3.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/1.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/5.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/6.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/2.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-After.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/doxygen -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/doxygen/README -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/doxygen/Doxyfile -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/ChooseMemoryOptions.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignmentUnmarked.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot.png -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Running.html -- Installing: /<>/debian/tmp/<>/obj-x86_64-linux-gnu/./shasta-install/docs/Configurations.html make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/<>' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:418: renaming shasta.so to shasta.cpython-312-x86_64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/<>' patchelf \ --set-soname shasta.cpython-312-x86_64-linux-gnu.so \ /<>/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so make[1]: Leaving directory '/<>' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/<>' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//<> dh_missing --list-missing make[1]: Leaving directory '/<>' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a 429c3b8e1d5fa9c70aa8e7eb44add0b6bf67544e b34960fdee0e1f343a5bc5434b8b1785cdf1a197 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/<>' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/<>/obj-x86_64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-312-x86_64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/<>' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-shasta (in debian/python3-shasta); do_strip: , oemstrip: pkgstriptranslations: processing shasta (in debian/shasta); do_strip: , oemstrip: pkgstriptranslations: processing python3-shasta-doc (in debian/python3-shasta-doc); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-shasta/DEBIAN/control, package python3-shasta, directory debian/python3-shasta INFO: pkgstripfiles: waiting for lock (python3-shasta) ... pkgstripfiles: processing control file: debian/shasta/DEBIAN/control, package shasta, directory debian/shasta Searching for duplicated docs in dependency python3-shasta... symlinking changelog.Debian.gz in shasta to file in python3-shasta pkgstripfiles: Running PNG optimization (using 4 cpus) for package shasta ... pkgstripfiles: No PNG files. dpkg-deb: building package 'shasta' in '../shasta_0.11.1-5_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing shasta-dbgsym (in debian/.debhelper/shasta/dbgsym-root); do_strip: , oemstrip: pkgstripfiles: Truncating usr/share/doc/python3-shasta/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-shasta ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.11.1-5_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/shasta/dbgsym-root/DEBIAN/control, package shasta-dbgsym, directory debian/.debhelper/shasta/dbgsym-root dpkg-deb: building package 'shasta-dbgsym' in 'debian/.debhelper/scratch-space/build-shasta/shasta-dbgsym_0.11.1-5_amd64.deb'. Renaming shasta-dbgsym_0.11.1-5_amd64.deb to shasta-dbgsym_0.11.1-5_amd64.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-shasta-dbgsym (in debian/.debhelper/python3-shasta/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-shasta/dbgsym-root/DEBIAN/control, package python3-shasta-dbgsym, directory debian/.debhelper/python3-shasta/dbgsym-root dpkg-deb: building package 'python3-shasta-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-shasta/python3-shasta-dbgsym_0.11.1-5_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " Renaming python3-shasta-dbgsym_0.11.1-5_amd64.deb to python3-shasta-dbgsym_0.11.1-5_amd64.ddeb pkgstripfiles: processing control file: debian/python3-shasta-doc/DEBIAN/control, package python3-shasta-doc, directory debian/python3-shasta-doc pkgstripfiles: Truncating usr/share/doc/python3-shasta-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package python3-shasta-doc (to save build time) dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.11.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.11.1-5_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../shasta_0.11.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-09T05:32:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ shasta_0.11.1-5_amd64.changes: ------------------------------ Format: 1.8 Date: Wed, 08 May 2024 22:02:57 +0200 Source: shasta Binary: python3-shasta python3-shasta-doc shasta Built-For-Profiles: noudeb Architecture: amd64 all Version: 0.11.1-5 Distribution: oracular-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: python3-shasta - nanopore whole genome assembly (dynamic library) python3-shasta-doc - nanopore whole genome assembly (documentation) shasta - nanopore whole genome assembly (binaries and scripts) Closes: 1069370 Changes: shasta (0.11.1-5) unstable; urgency=medium . * d/rules: meddle with RPATH only after dh_shlibdeps. (Closes: #1069370) Checksums-Sha1: f2ad4a5232de9a8407b5ae40292b416715a4e6c3 126936 python3-shasta-dbgsym_0.11.1-5_amd64.ddeb 6692bc1163ba98e029b9a8aa0ac5a4f2ac7432a9 24406 python3-shasta-doc_0.11.1-5_all.deb a68d38e54ac4fe7bd867d7ad8070f357dc6f958e 2270542 python3-shasta_0.11.1-5_amd64.deb a25eb266d666ab202f43dc8ace692ec452efd7c9 8828 shasta-dbgsym_0.11.1-5_amd64.ddeb 51fa16249364c325cd44cbb5e69143ff7a12452c 17493 shasta_0.11.1-5_amd64.buildinfo df30ced5ade72836898f70e4a8f67abc6dcf92d6 654904 shasta_0.11.1-5_amd64.deb Checksums-Sha256: 99bda6453796250fec55e9ba4cd470961faf3789c666acfba798800d695ebf3b 126936 python3-shasta-dbgsym_0.11.1-5_amd64.ddeb b455a3c4238ad4aa87a2235a7ebfa37387563852cf6f19eb9974252678d98123 24406 python3-shasta-doc_0.11.1-5_all.deb 0b33312c0a03391fca8e661b98bb0d344b0ae5f2f3e8d5d9ceb31939f286f42f 2270542 python3-shasta_0.11.1-5_amd64.deb d57f2aec0f4421167814d00cc52ec050989c541713f638b067e24ca22258d7a5 8828 shasta-dbgsym_0.11.1-5_amd64.ddeb 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+------------------------------------------------------------------------------+ Format: 1.0 Source: shasta Binary: python3-shasta python3-shasta-dbgsym python3-shasta-doc shasta shasta-dbgsym Architecture: all amd64 Version: 0.11.1-5 Checksums-Md5: 4ae5813c3a9dc804c3c0c997f4cf6694 126936 python3-shasta-dbgsym_0.11.1-5_amd64.ddeb 2e98825e4b753e8fb779d938ed42b30f 24406 python3-shasta-doc_0.11.1-5_all.deb e5ae8c792b326c53741b35d548b24e72 2270542 python3-shasta_0.11.1-5_amd64.deb 7e442a0e218d559afac0c55606cc5849 8828 shasta-dbgsym_0.11.1-5_amd64.ddeb 70babc8eef290978c0b68fe291a458fe 654904 shasta_0.11.1-5_amd64.deb Checksums-Sha1: f2ad4a5232de9a8407b5ae40292b416715a4e6c3 126936 python3-shasta-dbgsym_0.11.1-5_amd64.ddeb 6692bc1163ba98e029b9a8aa0ac5a4f2ac7432a9 24406 python3-shasta-doc_0.11.1-5_all.deb a68d38e54ac4fe7bd867d7ad8070f357dc6f958e 2270542 python3-shasta_0.11.1-5_amd64.deb a25eb266d666ab202f43dc8ace692ec452efd7c9 8828 shasta-dbgsym_0.11.1-5_amd64.ddeb 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base-passwd (= 3.6.3build1), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-x86-64-linux-gnu (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu6), bsdutils (= 1:2.39.3-9ubuntu6), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), chrpath (= 0.16-2build1), cmake (= 3.29.2-2), cmake-data (= 3.29.2-2), coreutils (= 9.4-3ubuntu6), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-24ubuntu1), cpp-13-x86-64-linux-gnu (= 13.2.0-24ubuntu1), cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86ubuntu1), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build2), dh-autoreconf (= 20), dh-exec (= 0.29build1), dh-python (= 6.20240422), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1build1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.6ubuntu10), dpkg-dev (= 1.22.6ubuntu10), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5build1), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-24ubuntu1), g++-13-x86-64-linux-gnu (= 13.2.0-24ubuntu1), g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-24ubuntu1), gcc-13-base (= 13.2.0-24ubuntu1), gcc-13-x86-64-linux-gnu (= 13.2.0-24ubuntu1), gcc-14-base (= 14-20240429-1ubuntu1), gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu2), gettext-base (= 0.21-14ubuntu2), gfortran (= 4:13.2.0-7ubuntu1), gfortran-13 (= 13.2.0-24ubuntu1), gfortran-13-x86-64-linux-gnu (= 13.2.0-24ubuntu1), gfortran-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), grep (= 3.11-4build1), groff-base (= 1.23.0-4), gzip (= 1.12-1ubuntu3), hostname (= 3.23+nmu2ubuntu2), ibverbs-providers (= 50.0-2build2), icu-devtools (= 74.2-1ubuntu3), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3build2), libamdhip64-5 (= 5.7.1-3), libarchive-zip-perl (= 1.68-1), 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libboost-iostreams1.83.0 (= 1.83.0-2.1ubuntu3), libboost-json-dev (= 1.83.0.1ubuntu2), libboost-json1.83-dev (= 1.83.0-2.1ubuntu3), libboost-json1.83.0 (= 1.83.0-2.1ubuntu3), libboost-locale-dev (= 1.83.0.1ubuntu2), libboost-locale1.83-dev (= 1.83.0-2.1ubuntu3), libboost-locale1.83.0 (= 1.83.0-2.1ubuntu3), libboost-log-dev (= 1.83.0.1ubuntu2), libboost-log1.83-dev (= 1.83.0-2.1ubuntu3), libboost-log1.83.0 (= 1.83.0-2.1ubuntu3), libboost-math-dev (= 1.83.0.1ubuntu2), libboost-math1.83-dev (= 1.83.0-2.1ubuntu3), libboost-math1.83.0 (= 1.83.0-2.1ubuntu3), libboost-mpi-dev (= 1.83.0.1ubuntu2), libboost-mpi-python-dev (= 1.83.0.1ubuntu2), libboost-mpi-python1.83-dev (= 1.83.0-2.1ubuntu3), libboost-mpi-python1.83.0 (= 1.83.0-2.1ubuntu3), libboost-mpi1.83-dev (= 1.83.0-2.1ubuntu3), libboost-mpi1.83.0 (= 1.83.0-2.1ubuntu3), libboost-nowide-dev (= 1.83.0.1ubuntu2), libboost-nowide1.83-dev (= 1.83.0-2.1ubuntu3), libboost-nowide1.83.0 (= 1.83.0-2.1ubuntu3), libboost-numpy-dev (= 1.83.0.1ubuntu2), libboost-numpy1.83-dev (= 1.83.0-2.1ubuntu3), libboost-numpy1.83.0 (= 1.83.0-2.1ubuntu3), libboost-program-options-dev (= 1.83.0.1ubuntu2), libboost-program-options1.83-dev (= 1.83.0-2.1ubuntu3), libboost-program-options1.83.0 (= 1.83.0-2.1ubuntu3), libboost-python-dev (= 1.83.0.1ubuntu2), libboost-python1.83-dev (= 1.83.0-2.1ubuntu3), libboost-python1.83.0 (= 1.83.0-2.1ubuntu3), libboost-random-dev (= 1.83.0.1ubuntu2), libboost-random1.83-dev (= 1.83.0-2.1ubuntu3), libboost-random1.83.0 (= 1.83.0-2.1ubuntu3), libboost-regex-dev (= 1.83.0.1ubuntu2), libboost-regex1.83-dev (= 1.83.0-2.1ubuntu3), libboost-regex1.83.0 (= 1.83.0-2.1ubuntu3), libboost-serialization-dev (= 1.83.0.1ubuntu2), libboost-serialization1.83-dev (= 1.83.0-2.1ubuntu3), libboost-serialization1.83.0 (= 1.83.0-2.1ubuntu3), libboost-stacktrace-dev (= 1.83.0.1ubuntu2), libboost-stacktrace1.83-dev (= 1.83.0-2.1ubuntu3), libboost-stacktrace1.83.0 (= 1.83.0-2.1ubuntu3), libboost-system-dev (= 1.83.0.1ubuntu2), 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3.12.3-0ubuntu1), python3-docutils (= 0.20.1+dfsg-3), python3-idna (= 3.6-2), python3-imagesize (= 1.4.1-1), python3-jinja2 (= 3.1.3-1), python3-markupsafe (= 2.1.5-1build2), python3-minimal (= 3.12.3-0ubuntu1), python3-packaging (= 24.0-1), python3-pkg-resources (= 68.1.2-2ubuntu1), python3-pybind11 (= 2.11.1-2), python3-pygments (= 2.17.2+dfsg-1), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-setuptools (= 68.1.2-2ubuntu1), python3-snowballstemmer (= 2.2.0-4build1), python3-sphinx (= 7.2.6-6), python3-urllib3 (= 2.0.7-1), python3.12 (= 3.12.3-1), python3.12-dev (= 3.12.3-1), python3.12-minimal (= 3.12.3-1), rapidjson-dev (= 1.1.0+dfsg2-7.2), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sgml-base (= 1.31), sphinx-common (= 7.2.6-6), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), tzdata (= 2024a-4ubuntu1), util-linux (= 2.39.3-9ubuntu6), xml-core (= 0.19), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1715198577" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-shasta-doc_0.11.1-5_all.deb ----------------------------------- new Debian package, version 2.0. size 24406 bytes: control archive=1442 bytes. 1383 bytes, 34 lines control 1499 bytes, 17 lines md5sums Package: python3-shasta-doc Source: shasta Version: 0.11.1-5 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 288 Depends: libjs-sphinxdoc (>= 7.2.2) Recommends: shasta, python3-shasta Built-Using: sphinx (= 7.2.6-6) Section: doc Priority: optional Multi-Arch: foreign Homepage: https://github.com/chanzuckerberg/shasta Description: nanopore whole genome assembly (documentation) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the documentation for the shasta and python3-shasta packages. drwxr-xr-x root/root 0 2024-05-08 20:02 ./ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc-base/ -rw-r--r-- root/root 296 2024-05-08 20:02 ./usr/share/doc-base/python3-shasta-doc.shasta drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/ -rw-r--r-- root/root 1435 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/changelog.Debian.gz -rw-r--r-- root/root 2607 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/copyright drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_sources/ -rw-r--r-- root/root 522 2022-11-08 17:22 ./usr/share/doc/python3-shasta-doc/html/_sources/index.rst.txt drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/ -rw-r--r-- root/root 15094 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/basic.css -rw-r--r-- root/root 4302 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/classic.css lrwxrwxrwx root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js -rw-r--r-- root/root 323 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/documentation_options.js -rw-r--r-- root/root 286 2024-03-21 21:19 ./usr/share/doc/python3-shasta-doc/html/_static/file.png lrwxrwxrwx root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js -rw-r--r-- root/root 90 2024-03-21 21:19 ./usr/share/doc/python3-shasta-doc/html/_static/minus.png -rw-r--r-- root/root 90 2024-03-21 21:19 ./usr/share/doc/python3-shasta-doc/html/_static/plus.png -rw-r--r-- root/root 4929 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/pygments.css lrwxrwxrwx root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js lrwxrwxrwx root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/sidebar.js -> ../../../../javascript/sphinxdoc/1.0/sidebar.js lrwxrwxrwx root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js -rw-r--r-- root/root 22631 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/genindex.html -rw-r--r-- root/root 181701 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/index.html -rw-r--r-- root/root 1189 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/objects.inv -rw-r--r-- root/root 3567 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/py-modindex.html -rw-r--r-- root/root 3324 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/search.html -rw-r--r-- root/root 24990 2024-05-08 20:02 ./usr/share/doc/python3-shasta-doc/html/searchindex.js python3-shasta_0.11.1-5_amd64.deb --------------------------------- new Debian package, version 2.0. size 2270542 bytes: control archive=1238 bytes. 1572 bytes, 31 lines control 259 bytes, 3 lines md5sums 63 bytes, 1 lines shlibs 75 bytes, 2 lines triggers Package: python3-shasta Source: shasta Version: 0.11.1-5 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7686 Depends: python3 (<< 3.13), python3 (>= 3.12~), libblas3 | libblas.so.3, libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.4), liblapack3 | liblapack.so.3, libpng16-16t64 (>= 1.6.2), libpython3.12t64 (>= 3.12.1), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 13.1), ncbi-blast+ Section: python Priority: optional Homepage: https://github.com/chanzuckerberg/shasta Description: nanopore whole genome assembly (dynamic library) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the dynamic library that can be interfaced and imported within Python. drwxr-xr-x root/root 0 2024-05-08 20:02 ./ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/lib/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 7852592 2024-05-08 20:02 ./usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/python3-shasta/ -rw-r--r-- root/root 1432 2024-05-08 20:02 ./usr/share/doc/python3-shasta/changelog.Debian.gz -rw-r--r-- root/root 2607 2024-05-08 20:02 ./usr/share/doc/python3-shasta/copyright shasta_0.11.1-5_amd64.deb ------------------------- new Debian package, version 2.0. size 654904 bytes: control archive=5591 bytes. 1422 bytes, 30 lines control 13903 bytes, 165 lines md5sums Package: shasta Version: 0.11.1-5 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2600 Depends: libboost-chrono1.83.0t64 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), python3-shasta (= 0.11.1-5) Section: science Priority: optional Homepage: https://github.com/chanzuckerberg/shasta Description: nanopore whole genome assembly (binaries and scripts) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the executable binaries (tools) and accommodating scripts. drwxr-xr-x root/root 0 2024-05-08 20:02 ./ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/bin/ -rwxr-xr-x root/root 337369 2024-05-08 20:02 ./usr/bin/shasta drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-05-08 20:02 ./usr/share/doc/shasta/ -rw-r--r-- root/root 1106 2022-11-08 17:22 ./usr/share/doc/shasta/AlignOrientedReads.py -rw-r--r-- root/root 942 2022-11-08 17:22 ./usr/share/doc/shasta/AlignOrientedReads1.py -rw-r--r-- root/root 1898 2022-11-08 17:22 ./usr/share/doc/shasta/AlignOrientedReads4.py -rw-r--r-- root/root 636 2022-11-08 17:22 ./usr/share/doc/shasta/AlignPseudoPaths.py -rw-r--r-- root/root 958 2022-11-08 17:22 ./usr/share/doc/shasta/AnalyzeAlignmentMatrix.py -rw-r--r-- root/root 310 2022-11-08 17:22 ./usr/share/doc/shasta/AnalyzeAssemblyGraphBubbles.py 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+------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 113072 Build-Time: 304 Distribution: oracular-proposed Host Architecture: amd64 Install-Time: 35 Job: shasta_0.11.1-5.dsc Machine Architecture: amd64 Package: shasta Package-Time: 340 Source-Version: 0.11.1-5 Space: 113072 Status: successful Version: 0.11.1-5 -------------------------------------------------------------------------------- Finished at 2024-05-09T05:32:05Z Build needed 00:05:40, 113072k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28433581 Scanning for processes to kill in build PACKAGEBUILD-28433581